US 5,656,493 AGrant
System for Automated Performance of the Polymerase Chain Reaction
Issue Date:1997-08-12
•17 Claims
•19 Drawing Sheets
Abstract
There is disclosed herein a machine for performing nucleic acid amplification under computer control. The machine utilizes any one of a number of heating and cooling systems under control of a host computer which directs the heating and cooling systems to heat and cool a reaction-chamber-containing heat exchanger at appropriate times in the process. The reaction chambers are pre-loaded with the nucleic acid(s) to be amplified, a thermostable enzyme to catalyze polymerization, specific oligonucleotide primers, and four different nucleotide triphosphates. Also disclosed is the process for the amplification chain reaction implemented by the machine, which utilizes a thermostable enzyme.
Metadata
Assignee
- The Perkin-Elmer Corporation
Inventors
- Kary B. Mullis
- Larry Johnson
- Richard A. Leath
- Timothy J. Wennberg
- Louis M. Mezei
- Joseph T. Widunas
Application Information
Application Number:US 1995057
Filing Date:1994-02-18
Priority Date:1985-03-28
Art Unit:187
Classifications
IPC:
C12M 302C12M 100G01N 2100C12N 1500
Field of Search:
4355369354222366;183;91.1;91.2;286.11;287.1;287.2;285.123.1;24.3;24.33;25.376;77;85;87;8850;6291 R;97;1 C;15 BG
Patent Drawings (19 sheets)
Description
Background of the Invention
The invention pertains to the field of chain reactions for amplifying DNA or RNA (nucleic acids), and, more particularly, to the field of machines for automatically performing this process through temperature cycling.
Methods described in the past for synthesizing nucleic acid sequences from an existing sequence, for example, the phosphodiester and phosphotriester methods [see Narang et al., Meth. Entymol. 68, 90 (1979); and Brown et al., Meth. Enzymol. 68, 109 (1979), respectively], are not practical to produce large amounts of nucleic acid sequences. Such methods are laborious and time-consuming, require expensive equipment and reagents, and have a low overall efficiency.
There are methods for producing nucleic acid sequences in large amounts from small amounts of an existing sequence. Such methods involve cloning of a nucleic acid sequence in an appropriate host system, and culturing the host, wherein the vector in which the nucleic acid sequence has been inserted is replicated, resulting in copies of the vector and hence the Sequence. See T. Maniatis, et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, pp. 390-401 (1982); and U.S. Pat. Nos. 4,416,988 and 4,403,036. The original sequence can also be organically synthesized before insertion in a vector. See U.S. Pat. No. 4,293,652.
A method, described by Saiki et al., Science, 230, 1530-1534 (1985), has been devised for amplifying one or more specific nucleic acid sequences or a mixture thereof using primers, nucleotide triphosphates, and an agent for polymerization, such as DNA polymerase, The extension product of one primer, when hybridized to the other, becomes a template for the production of the desired specific nucleic acid sequence, and vice versa. The process is repeated as often as necessary to produce the desired amount of the sequence. The method is referred to in the Science article as Polymerase Chain Reaction or "PCR".
This method is especially useful for performing clinical tests on the DNA or RNA from a fetus or other donor where large amounts of the DNA or RNA are not readily available and more DNA or RNA must be manufactured to have a sufficient amount to perform tests. The presence of diseases which have unique DNA or RNA signatures can be detected by amplifying a nucleic acid sample from a patient and using various probe procedures to assay for the presence of the nucleic acid sequence being detected in the test. Such test might be prenatal diagnosis of sickle cell anemia, as described by Saiki et al., supra, where the amplification of specific B-globin target sequences in genomic DNA resulted in the exponential increase (220,000 times) of target DNA copies, increasing sensitivity and speed while reducing the complexity of diagnosis. Another test is the diagnosis of the AIDS virus, which is thought to alter the nucleic acid sequence of its victims.
Five patent applications which describe the amplification process, PCR, are U.S. patent application Ser. No. 818,127, filed Jan. 10, 1986, now abandoned, U.S. Ser. No. 716,982, filed Mar. 28, 1985, now U.S. Pat. No. 4,683,194, U.S. Ser. No. 791,308, filed Oct. 25, 1985, now U.S. Pat. No. 4,683,202, U.S. Ser. No. 828,144, filed Feb. 7, 1986, now U.S. Pat. No. 4,683,195, and U.S. Ser. No. 839,331, filed Mar. 13, 1986, now abandoned, the disclosures of all of which are incorporated herein by reference.
The amplification method, PCR, bears some similarity to the molecular cloning methods described above, but does not involve propagation of a host organism, avoiding the hazards and inconvenience therein involved. In addition, the amplification method does not require synthesis of nucleic acid sequences unrelated to the desired sequence, and thereby obviates the need for extensive purification of the product from a complicated biological mixture. Finally, the amplification is more efficient than the alternative methods for producing large amounts of nucleic acid sequences from a target sequence and for producing such sequences in a comparatively short period of time.
At first, the amplification procedure, PCR, described above was carried out by hand in the laboratories. The manual process involves a great deal of repetitive liquid handling steps and incubations at controlled temperatures. This is not only time-consuming and tedious, but it is also subject to error caused by human operator attention span drift. Such errors could result in a misdiagnosis of a genetic birth defect and an unnecessary abortion or the lack of an abortion where a birth defect exists. Further, such errors could result in misdiagnosis of sickle cell anemia or other genetic disorders.
Further, certain nucleic acids amplify more efficiently than others, so some nucleic acid sequence amplifications require more amplification cycles than others because the cost of laboratory labor can be high, and the risks to which a laboratory is subjected are high in case of error in erroneously performing amplification, there has arisen a need for a system which can automate the amplification process.
Summary of the Invention
The amplification process, PCR, maybe conducted continuously. In one embodiment of an automated process, the reaction may be cycled through a denaturing region, a reagent addition region, and a reaction region. In another embodiment, the enzyme used for the synthesis of primer extension products can be immobilized in a column. The other reaction components can be continuously circulated by a pump through the column and a heating coil in series; thus the nucleic acids produced can be repeatedly denatured without inactivating the enzyme.
One embodiment of a machine for automating the amplification process utilizes a liquid handling system under computer control to make liquid transfers of enzyme stored at a controlled temperature in a first receptacle into a second receptacle whose temperature is controlled by the computer to conform to a certain incubation profile. The second receptacle stores the nucleic acid sequence to be amplified plus certain reagents. The computer includes a user interface through which a user can enter process parameters which control the characteristics of the various steps in the sequence such as the times and temperatures of incubation, the amount of enzyme to transfer on each cycle into the second receptacle from the first receptacle, as well as the number of cycles through the amplification sequence that the user desires the machine to perform. The first and second receptacles may be controlled in temperature by use of three circulating fluid reservoirs and solenoid operated valves. Of course, any other method for controlling the temperatures of the receptacles will also work for purposes of the invention, and the invention is not limited to the use of heated and chilled circulating fluids. These solenoid operated valves are coupled to the computer such that the proper temperature fluid can be directed through the supporting structure for the first and second receptacles at the proper times in the PCR sequence under computer control. The first receptacle, which stores enzyme to be added to the reaction well of the second receptacle, is kept at a constant temperature. The second receptacle, which is where the PCR reaction occurs, is switched under computer control between two temperatures by the transmission of a control signal to the solenoid operated valves at the proper time in the sequence to gate either the hot fluid or the cold fluid through the support structure of the second receptacle.
While the above-described machine increases the amount of nucleic acid sequence which can be amplified per unit of labor, thereby decreasing the possibility of error, it involves liquid handling, where reagents must be continuously transferred at various cycles. There is a need also for a machine which not only automates the amplification process, but also makes it faster and more convenient. This can be accomplished using an enzyme which is thermostable, i.e., will not break down when subjected to denaturing temperatures.
A second embodiment of the invention utilizes a temperature-cycling instrument for implementing the amplification process when a thermostable enzyme is employed. The use of a thermostable enzyme avoids the need for liquid transferring of the enzyme, which is necessitated when the enzyme is unstable in the presence of heat. As used herein to describe enzymes, "thermostable" means stable at temperatures above 90.degree. C. and "heat-stable" means stable at temperatures 65.degree.-90.degree. C.
More specifically, this second embodiment of the invention herein relates to an apparatus for performing automated amplification of at least one specific nucleic acid sequence comprising:
a heat-conducting container for holding a reaction mixture comprising a thermostable enzyme, said nucleic acid sequence(s) to be amplified, four different nucleotide triphosphates, and one oligonucleotide primer for each different specific sequence being amplified, wherein each primer is selected to be substantially complementary to different strands of each specific sequence, such that the extension product synthesized from one primer, when it is separated from its complement, can serve as a template for synthesis of the extension product of the other primer;
means for heating, cooling, and maintaining said container to or at any of a plurality of predetermined (user-defined) temperatures and having an input for receiving a control signal controlling which of said predetermined temperatures at or to which said container is heated, cooled, or maintained; and
a computer means, coupled to the input of said means for heating and cooling to generate the proper control signals to control the temperature levels, temperature rate-of-change ramps, and timing of the incubations at certain temperature levels.
A variation of the second embodiment of this invention also provides an apparatus for performing automated amplification of at least one specific nucleic acid sequence comprising:
a first means for holding a reaction mixture comprising said nucleic acid sequence(s) to be amplified, four different nucleotide triphosphates, a thermostable enzyme, and one oligonucleotide primer for each different specific sequence being amplified, wherein each primer is selected to be substantially complementary to different strands of each specific sequence, such that the extension product synthesized from one primer, when it is separated from its complement, can serve as a template for synthesis of the extension product of the other primer, said holding being carried out at any selected temperature or plurality of temperatures; and
a second means for automatically performing a predetermined sequence of steps including causing said first means to heat its contents for a first period and to cool its contents for a second period.
In yet another variation of the second embodiment, the invention herein provides an apparatus for performing an assay including heating and cooling steps as part of the sequence of steps of the assay comprising:
means for performing the sequence of steps wherein heating and cooling steps would be beneficial; and
means in said means for performing for causing said heating and cooling steps to be performed at the proper point in the sequence of steps comprising the assay.
In a third embodiment, this invention provides a method for amplifying at least one specific nucleic acid sequence comprising the steps of:
using a computer-directed machine to heat to a predetermined temperature for a predetermined time a sample of the nucleic acid sequence(s) to be amplified, four different nucleotide triphosphates, a thermostable enzyme, and one oligonucleotide primer for each different specific sequence being amplified, wherein each primer is selected to be substantially complementary to different strands of each specific sequence, such that the extension product synthesized from one primer, when it is separated from its complement, can serve as a template for synthesis of the extension product of the other primer (hereafter the mixture); and
using a computer-directed machine to chill the mixture to a predetermined temperature.
In a variation of the third embodiment, this invention provides a method of amplifying at least one specific nucleic acid sequence comprising the steps of:
a) using a computer-directed machine to issue a heat signal to a heating apparatus to cause a reaction chamber to be heated for a predetermined time to and/or at a predetermined temperature, wherein said reaction chamber contains the mixture described above;
b) using a computer-directed machine to issue a cool signal to a cooling apparatus to cause said reaction chamber to be cooled for a predetermined time to and/or at a predetermined temperature; and
c) using a computer-directed machine to repeat the cycle consisting of steps a through c when the elapsed time for the active cooling signal equals a user-defined time if the number of cycles performed thus far is less than a user-defined number of cycles.
The apparatus herein also generally contains a power supply for operation, a structural system to contain all the elements of the apparatus, and a keyboard and display panel to allow control of the apparatus by an operator.
The receptacle which holds the reagents where the reaction occurs has its temperature controlled by a computer to conform to a certain incubation profile defined by the user. Circulating fluid reservoirs (three for the first embodiment, two for the second) and solenoid operated valves, or any other method, may be employed to control temperature. The Peltier heat pumps available from Materials Electronics Products Corporation in Trenton, N.J., may also be used, as well as a water heat exchanger or any other heating and cooling system which may be controlled by a computer.
If solenoid-operated valves are employed, they are coupled to the computer such that the proper temperature fluid can be directed through the supported structure for the heat-conducting receptacle at the proper times in the amplification process under computer control. The receptacle is switched under computer control between two temperatures by the transmission of a control signal to the solenoid-operated valves at the proper time in the sequence to gate either the hot fluid or the cold fluid through the support structure of the receptacle. A temperature sensor coupled to the reaction chamber and the computer is used to provide a signal indicating the actual temperature. The computer compares the actual temperature to the desired temperature. An error signal is generated in this fashion which is used to control the apparatus which heats and cools the reaction chambers. The computer also keeps track of the elapsed time at particular temperatures to implement the incubation periods in the protocol.
The basic process that the machine performs to implement the amplification protocol after the starting materials are loaded into the reaction well, in one embodiment using water baths, is as follows.
The computer signals the solenoid-operated valves to gate the hot fluid through the supporting structure for the reaction chamber thereby heating the contents of the reaction well to the temperature of the hot fluid.
The amount of time the hot fluid is gated "on" is measured by an elapsed time counter.
The computer compares the elapsed time the hot fluid has been gated "on" to a variable set in memory. In the preferred embodiment, this variable can be changed by the user through the user interface. In other embodiments, it may be fixed.
When the elapsed time matches the variable for the hot incubation, the computer sends a signal to the solenoid-operated valves to stop the hot fluid flow and gate the cold fluid flow through the supporting structure for the reaction vessel.
In embodiments using temperature control feedback instead of empirically determined "on" times for the hot and cold fluids, a temperature profile versus time for the reaction chamber is programmed into the computer via the user interface. This causes the computer to control the reaction or reagent vessel temperature in the sequence required by the particular amplification reaction parameters. Such an embodiment uses a thermistor or other temperature sensor to monitor the temperature of the reaction chamber and generates an error signal derived by comparing the actual temperature of the reaction chamber to the user-defined temperature profile. The error signal is used to control a heat pump or other heating and cooling apparatus to maintain the desired temperature profile during the high temperature heat-up and high temperature incubation and during the chill-down and low-temperature incubation.
On either temperature feedback or empirically determined time embodiments, the computer starts a timer and compares the elapsed time for hot or cold fluid flow or the elapsed time at a particular temperature to a user-defined variable stored in memory for each segment or leg in the temperature profile. These variables can be set by the user in the preferred embodiment through the user interface. In embodiments where no temperature sensor is used, the variable for proposed time of hot or cold fluid flow is empirically determined by the user as the time it takes to heat or cool the reaction vessel to a predetermined temperature from the starting temperature plus the desired incubation time.
The above temperature profile control apparatus and methods for embodiments using hot and cold fluid reservoirs and solenoid-operated valves are equally applicable to embodiments using Peltier heat pumps or other forms of heating and cooling apparatus coupled to the reaction chamber or chambers.
In the first embodiment with a liquid handler for enzyme addition, as soon as the elapsed time for gating the cold fluid matches the variable, the computer sends signals to the liquid handler to cause it to aspirate from the first receptacle an amount of enzyme controlled by a user defined variable stored in the computer memory and deposit it in the reaction well. In the preferred embodiment, the computer sends the proper signals to cause the liquid handler to mix the newly deposited enzyme with the pre-existing contents of the reaction well. When multiple rows of enzyme and multiple rows of reaction chambers are being used multiple rows of tips are used. Each row of tips is mapped to a specific row of enzyme and to a specific row of reaction chambers. Thus the tips in each row contact only the enzyme and nucleic acid from their specified rows of enzyme and reaction chambers. The tips from each row never contact either enzyme in wells that have been used to store enzyme transferred to other rows of reaction chambers with different nucleic acids therein and never contact the nucleic acid in other rows of reaction chambers other than the specifically designated row of reaction chambers. This prevents cross contamination and the attendant dangers posed thereby. Further, in the preferred embodiment, the tips are stored in storage wells which are completely enclosed such that each tip is separated by a physical barrier from each other tip. This prevents any enzyme or nucleic acid which clings to the tip after an enzyme transfer cycle from accidentally being splashed, thrown or blown onto other tips to cross contaminate them.
After the deposit of new enzyme, the computer starts a timer to measure the time of a cold incubation at the temperature of the cold fluid then flowing through the support structure of the reaction well. When the elapsed time matches a variable stored in the memory, preferably specified by the user, the first cycle is done.
For all embodiments, the above process repeats itself for the number of cycles specified by the user.
Brief Description of the Drawings
FIG. 1 is a general block diagram of a machine which can perform the amplification process using the thermostable enzyme and Peltier heat pumps to cycle the temperature of the reaction vessels.
FIG. 2 is a general block diagram of a machine which can perform the thermostable enzyme amplification process herein using water baths to cycle the temperature of the reaction vessels.
FIG. 3 is a diagram of a solid state heat pump and reaction chamber heat exchanger structure.
FIG. 4 is a schematic diagram of the interface unit for a solid state heat pump .
FIG. 5 is a diagram of a typical user-defined temperature profile.
FIG. 6A and FIG. 6B comprise a first part and a second part respectively, of a flow diagram for the control software for the empirical embodiments which do not use feedback of the actual reaction chamber temperature. FIGS. 6A and 6B may be referred to collectively herein as "FIG. 6".
FIG. 7A and FIG. 7B comprise a first part and a second part, respectively of a flow diagram for the control software for the preferred embodiments which use actual temperature feedback signals to monitor the actual temperature of the reaction chamber and 5 compare it to the desired temperature Profile. FIGS. 7A and 7B may be referred to collectively herein as "FIG. 7".
FIG. 8 is a general block diagram of a machine with liquid handling capability which can perform the PCR amplification process.
FIG. 9 is a flow chart of the process carried out by the machine of FIG. 8.
FIG. 10 is a drawing of a typical liquid handler which can be used for performing the liquid handling steps for the PCR amplification protocol.
FIG. 11 is a block diagram of the electronics which control the machine of FIG. 10 when doing the amplification protocol in any of the embodiments with a liquid handler described herein.
FIGS. 12A-12C are detailed flow charts of the amplification protocol steps carried out by the liquid handler using the software of microfiche Appendix A on either a PRO/PETTE.RTM. or a PRO/GROUP.RTM. machine.
FIG. 13 is a block diagram of another embodiment of a machine which can perform the amplification protocol, with liquid handling capability, with the computer monitoring the temperature of the reaction chamber and controlling the temperature along a user defined profile.
FIGS. 14A-14B are flow diagrams of the process flow implemented by the embodiment shown in FIG. 13.
Detailed Description of the Preferred Embodiments
Amplification Machine Using Thermostable Enzyme and No Liquid Handling
Referring to FIG. 1, there is shown a general block diagram of a machine which can perform the nucleic acid amplification process using the thermostable enzyme. The starting materials, comprised of the nucleic acid samples to be amplified and the necessary reagents, are initially loaded into a reaction well 40 in heat exchanger 10. The heat exchanger 10 supports the reaction well 40, which may be a recess machined into the heat exchanger, but preferably is a plastic container which holds the fluids involved in the reaction and which sits in a recess formed in heat exchanger 10 (hereafter sometimes referred to as plate 1). In the preferred embodiment, heat exchanger 10 is a heat-conducting block, preferably aluminum, with a plurality of recesses formed therein sized to allow a given number of 0.5 ml (milliliter) Eppendorf tubes to fit therein.
The purpose of the tubes is to line the reaction well to separate the fluids from the walls of the recesses in the heat exchanger 10 to avoid cross contamination when the same reaction well is used to amplify different nucleic acid sequences. The purpose of heat exchanger 10 is to support the tubes and to act as a heat exchanger to transfer thermal energy to and from the fluids stored in the tubes in the reaction wells, such that the reaction components may be incubated at various temperatures for user-defined times.
To that end, heat exchanger 10 must be structured in such a way that the fluids in the reaction wells such as the reaction chamber 40 may be heated and cooled at the appropriate times in the process and for the appropriate duration. Any structure or method may be used to perform this heating and cooling function such as electrical heating and refrigeration apparatus in or connected to heat exchanger 10 such as a heat pump or Peltier or Thompson solid state thermoelectronic coolers. It is only necessary that whatever apparatus is used for this heating and cooling be capable of reaching and sustaining the temperatures involved, and that the apparatus for heating and cooling achieve the user-defined temperature versus time profile.
In a preferred embodiment, pictured in FIG. 1, one such electrically driven heating and cooling apparatus is a Peltier solid state thermoelectric heat pump 12, a FRIGICHIP.RTM. device, available from Melcor Corporation in Trenton, N.J. A conventional heat pump using a compressor, an evaporator and a condenser will also work for heat pump 12. Solid state heat pumps such as Peltier devices are comprised of N and P type bismuth telluride in the form of oriented polycrystalline ingots forming back to back PN junctions and with the ends soldered to copper bus bars interfaced with ceramic plates. FIG. 3 shows such an arrangement. These heat pumps heat or cool by driving currents through them in particular, known ways to move heat in either direction between a heat sink 14 and the heat exchanger 10. These solid state heat pumps have been used by Gilford Instruments Corporation to heat and cool cuvettes, and are available in wattage ranges up to and including 150 watts. These devices are capable of cooling or heating a mass of material to which they are thermally coupled to temperatures in a range from -150 to +110 degrees centigrade. Such semiconductors could be thermally coupled in known ways to heat exchanger 10 or could be directly thermally coupled to the insert tubes or wells. Such semiconductors can be easily controlled to reach and maintain particular temperatures by modulating the currents which flow through them in accordance with the desired temperature level according to standard process control algorithms. The manner of designing such a solid state heat pump system is published in an application note on the FRIGICHIP.RTM. series FC solid state thermoelectric heat pump by Melcor (990 Spruce Street, Trenton, N.J. 08648 (609)-393-4178) which is hereby incorporated by reference.
In another embodiment, illustrated in FIG. 2, water baths 16 and 18 which maintain reservoirs of fluids at constant temperatures may be used. Again, heat exchanger 10 is an aluminum plate or some other metal with good heat-conducting properties. Passageways or channels 201 are machined or molded into the metal of the heat exchanger through which heated or cooled fluids may be pumped. In one embodiment of the machine pictured in FIG. 2, heat exchanger 10 has a fluid inlet coupled to a tube 42 and a fluid outlet coupled to a tube 44. These two tubes are coupled to the outputs of a fluid multiplexer 46. The fluid multiplexer has two pairs of input/output ports. One pair 47 is coupled to high temperature fluid conveyance tubes 48 and 50 and the other pair 49 is coupled to low temperature fluid conveyance tubes 52 and 54. Each pair of ports has one input channel and one output channel. For example, the first pair has its input channel coupled to tube 48 and its output channel coupled to tube 50. Likewise, the output pair of the fluid multiplexer 46 has one output channel, coupled to the tube 42, and one input channel, coupled to the tube 44. The purpose of the fluid multiplexer 46 is to couple selectively either the first input pair, tubes 48 and 50, or the second input pair, tubes 52 and 54, to the output pair 43 in accordance with a select signal on a line 56. If the first pair of ports 47 is selected, the tube 48 is coupled in fluid communication to the tube 42 through an internal fluid passage in the fluid multiplexer 46 in the form of a solenoid-operated valve designated SOV 1. Likewise, the tube 50 is coupled to the tube 44 through an internal fluid channel in the fluid control multiplexer 46 in the form of a solenoid-operated valve designated SOV 2. A similar connection occurs if the second pair of ports 49 is selected.
In this manner, the temperature of the heat exchanger 10 and the fluids stored in the tubes in the reaction wells such as the well 40 may be controlled by the state of a TEMP SELECT signal on the conductor 56. In one embodiment, the fluid multiplexer 46 is implemented with four solenoid-operated valves, designated SOV's 1 through 4, which are properly interconnected with the tubes 42, 44, 48, 50, 52 and 54. However, any apparatus that can perform the fluid switching noted above will suffice. Indeed, if a solid state or conventional heat pump 12 is used in connection with controlling the temperature of heat exchanger 10, the need for and expense of the fluid multiplexer 46 is eliminated.
The heated and cooled fluid flowing in the tubes coupled to the fluid multiplexer 46 is pumped from a high temerature fluid reservoir 16 and a low temperature fluid reservoir 18, respectively. The purpose of these reservoirs is to maintain a volume of fluid such as water or antifreeze at a constant temperature. Generally, the high temperature fluid is maintained at a constant temperature of 80.degree. to 105.degree. C., preferably 90.degree.-100.degree. C., and the low temperature fluid is maintained at a constant temperature of about 35.degree.-60.degree. C., preferably about 37.degree. C. to 50.degree. C. The reservoirs 16 and 18 are adjustable in terms of the temperatures at which they maintain their fluid reservoirs. Water bath 18 is preferably adjustable so as to be able to achieve a reservoir temerature anywhere in the range from -35.degree. to +150.degree. C. The water bath 18 preferably has a water capacity of 13 liters and a rapid chill-down feature so as to have a cool-down rate in excess of 100.degree. C. per minute. This helps minimize temperature stabilization time. Any type of fluid heating and cooling apparatus which can achieve and maintain such temperatures over the duration of the amplification process will suffice for purposes of the invention. In the preferred embodiment, VWR 1135 and VW2 1155 water baths are used.
The enzyme used in the amplification process is added to the other reagents in the reaction well 40 initially.
The enzyme employed herein is a thermostable enzyme, as defined hereinbelow, which can withstand the high temperatures employed to denature the nucleic acid strands. Therefore, a liquid handler is not necessary to add the thermostable enzyme to the reaction well at certain points in the temperature profile. The enzyme may stay in the reaction well 40 at all times.
Control over the temperature of the reaction vessel is maintained by the CPU 20 in the case of either the embodiment of FIG. 1 or the embodiment of FIG. 2. The CPU runs control program which will be described in more detail below. Basically, the control program, which is stored in a memory 24, controls the heat pump 12 or the fluid multiplexer 46. The user is interrogated by the control program through the CPU 20 and a display/keyboard user interface 22 regarding what temperature profile the user wishes to run. The user responds with temperatures on the desired profile and the times the user wants those temperatures to be achieved. These responses are read by the CPU 20 from a user interface 22. The queries to the user are displayed on the display of the user interface 22, and the user's responses are received via the keyboard thereof. User responses in the form of time and temperature checkpoints on the desired profile are stored in a RAM 24. A typical time versus temperature profile is shown in FIG. 5. The CPU then generates the proper control signals to cause heat to be added to or taken away from heat exchanger 10 to maintain the reaction vessel 40 on the desired temperature profile.
In the case of the embodiment shown in FIG. 1, the control signals generated by the CPU 20 to control the heat pump consist of a pulse train of pulse width modulated control pulses. These pulses are coupled to a heat pump interface circuit 26 on a line 56.
The circuitry of the heat pump interface is shown in more detail in FIG. 4. The purpose of this interface circuit is to convert the pulse width modulated control pulses at logic levels from the CPU into high current pulses of the same duration through the solid state heat pump 12. Four N channel MOSFET power transistors 30, 32, 34 and 36 are used for this purpose. These transistors are connected in a bridge arrangement with the solid state heat pump 12 as a load. This bridge reverses the direction of current flow through the load 12 under the influence of two control signals from the CPU on lines 39 and 40. When the cool control signal on line 40 is active, the transistors 34 and 32 are turned on and the transistors 30 and 36 are turned off. The reason for this is that the cool signal is coupled to the gate of the transistor 34 by the line 58 and turns this transistor on. The cool signal also turns on a transistor 62 which pulls the gate voltage on the line 64 down to ground potential thereby turning off transistor 36.
The heat control signal on line 39 is always in the opposite binary state as the cool control signal on line 40. Then cool is active, the gate 66 of transistor 30 is low at logic 0 and this transistor will be off. The logic 0 on line 66 also turns off a transistor 68, which allows the +15 volt voltage on line 70 to drive the gate 72 of the translator 32 to a logic 1 level. This turns on transistor 32, thereby completing a current path from right to left through the load 12, i.e., from line 70 and the power supply through the drain and source of transistor 34, through line 76, the load 12 and line 78, and through the drain and source of transistor 32 to ground.
The reverse situation occurs when the heat signal is active. In this case, transistors 30, 68 and 36 are on and transistors 34, 62 and 32 are off.
In the embodiment shown in FIG. 2, the interface circuit of FIG. 4 is not necessary. However, some solenoid driver interface will be necessary to allow the CPU to control the solenoid-operated valves. The design of a suitable interface will be well known to those skilled in the art.
The CPU 20 in the embodiments of either FIG. 1 or FIG. 2 may be any one of a number of different types of computers. It may be a custom designated computer, an off the shelf controller such as the Model 2010 PuP.TM. controller available from LFE Corporation in Clinton, Mass., or it may be an IBM or other personal computer, minicomputer or mainframe. Whatever type of computer is used, it must be capable of accepting data from the user regarding the desired temperature profile either in real time or at the time the computer is installed. There should be some mechanism to calculate a "set point" in embodiments using actual temperature sensors such as the sensors 80 in FIGS. 1 and 2. A "set point" is a target temperature taken from the user-defined temperature profile which can be used in calculating an error signal based upon the error between the actual temperature and the target temperature. Refer now to typical temperature profile illustrated in FIG. 5. Typical user-defined temperature profile checkpoints are shown as small circles. Checkpoint 1 is characterized by a temperature level L.sub.o at the reaction vessel 40 at time T.sub.o. Checkpoint 2 is characterized by a temperature level L.sub.2 at a later time T.sub.2. Checkpoint 3 is characterized by the existence of a temperature level L.sub.2 at the reaction vessel 40 at a time T.sub.2 and so on. The sections between checkpoints will be called "legs".
The CPU 20, in embodiments that do not use actual temperature sensors, must be programmed to keep track of the time during which heating or cooling action takes place. Further, the CPU must be capable of storing one or more empirically determined times against which actual elapsed time during a heating or cooling leg may be compared. These empirically determined times are experimentally determined by the user. Typically the user will set a certain current flow during the design of the solid state heat pump interface of FIG. 4, and this current flow will be used for all heating and cooling in the embodiment of FIG. 1. In the case of the embodiment of FIG. 2, the user must set the temperature level of the hot and cold reservoirs 16 and 18. The fixed current in the case of the embodiment of FIG. 1 and the fixed temperature level for the reservoirs in the case of the embodiment of FIG. 2 will establish a user-defined heating or cooling rate of change for a given mass of the heat exchanger 10 and reaction vessel and contents. The user will then define the desired checkpoints and determine the times it takes to heat or cool to these checkpoints at the fixed heating or cooling rate. If the times taken to reach the checkpoints are not acceptable, the heating or cooling rate must be adjusted until the times are right. Of course, this approach is not very flexible if the heating or cooling rate cannot be adjusted in real time, since the slope of the heating and cooling legs must always be the same using these embodiments, which will be referred to as the "empirical" class of embodiments.
An alternative empirical type embodiment class is to program the CPU 20 to use different heating and cooling rates on each leg. This allows each leg to have a different slope. This may be accomplished using pulse width modulation, but not using any temperature sensor and actual temperature feedback (illustration of the temperature sensors in dashed lines is intended to symbolize these embodiments) in either of the embodiments of FIGS. 1 and 2. In these alternative embodiments, the heating or cooling current flow (or fluid flow in the case of the embodiment of FIG. 2) is a stream of pulses. The duty cycle is controlled by the CPU 20 such that if a greater heating or cooling rate is needed, the "on" time of the pulses is increased. The reverse situation applies if the heating or cooling rate is to be decreased. In these embodiments, the user has more freedom to adjust the temperature profile because the empirical time and heating and cooling rate may both be adjusted until the interval between and temperature levels at the checkpoints are as desired.
Generally, this requires more work on the part of the user than the preferred embodiment and is not as accurate. The reason is that once the user establishes a fixed heating or cooling rate for each leg, that rate is fixed for that leg and cannot be altered in real time to account for changing conditions. That is, in these embodiments, the CPU 20 does not alter the heating and cooling rates in real time to correct for changing ambient conditions or other variations.
The preferred embodiment uses actual temperature feedback and a closed loop control system to control the heating and cooling rate. This allows real time error signal generation to conform the actual temperature profile to the desired temperature profile. To implement the preferred embodiment, the CPU 20 is programmed to prompt the user to enter "checkpoints" for the desired temperature profile. Then, the CPU 20 starts a clock running to measure elapsed time and periodically calculates "set points" based upon the desired temperature profile defined by the checkpoints. The calculated set points are targets to achieve and are used in another software routine to generate an error signal.
The error signal generation routine reads the actual temperature of the reaction chamber from the temperature sensor 80 and compares it to the desired temperature defined by the set point. Typical set points calculated for the temperature profile of FIG. 5 are shown by the three x's on leg 1 between checkpoints 1 and 2. The comparison yields an error signal which is used by a pulse width modulation routine to generate the control signals which cause heating or cooling of the reaction chamber by the heating and cooling apparatus.
The pulse width modulation routine calculates the necessary "on" time or duty cycle for the heat and cool control signals and determines which of these two control signals should be active. The proper control signals are then generated and written to the solid state heat pump interface 26 or to the fluid multiplexer or other heating and cooling apparatus.
The amplification process which the machine must perform for an empirical time embodiment not using a sensor 80 for the embodiments shown in FIGS. 1 and 2 is given in flow chart format in FIG. 6. The process starts at block 74 with a command from the user to start the amplification processing. Prior to this time the user must have loaded the proper enzyme into the reaction chambers 40 in heat exchanger 10 along with the nucleic acid sequence(s) to be amplified plus the proper reagents defined below.
Upon receiving the start command, the CPU 70, in a step 82, retrieves the first checkpoint data and issues the proper signal on the temperature select line 56 in FIG. 2 (the method of operation of FIG. 6 is equally applicable to the embodiment shown in FIG. 1) to cause the opening of the SOV pair 46 to heat the heat exchanger 10 to a high temperature equal to a user-defined level, which will be hereafter referred to as temperature variable L.sub.H. In some embodiments, temperature variable L.sub.H will not be a variable, but will be a constant fixed at the temperature of the high temperature reservoir 16. In other non-empirical embodiments using actual temperature feedback data, the variable L will be user-defined and the CPU 70 will monitor the temperature of the reaction chamber 40 and issue the proper command signal to the temperature control apparatus (solenoid-operated valves plus reservoirs or heat pump interface plus heat pump) to cause it to heat the heat exhanger 10 until the desired temperature is reached, and then will issue the proper commands to the temperature control apparatus to cause the desired temperature to be maintained. No monitoring of the temperature of heat exchanger 10 is done by the CPU 20 in the empirical embodiment currently under discussion. However, in the preferred embodiment, the temperature of the heat exchanger 10 and reaction vessel is monitored by the CPU 40, and an error signal is generated by comparison of the actual temperature to the calculated set points from the user-defined checkpoints to control the temperature of the heat exchanger 10 according to a user-defined time versus temperature profile.
The temperature of the reaction chamber 40 during this high-temperature incubation should be maintained at 80.degree.-105.degree. C., preferably 90.degree.-100.degree. C., The minimum temperature at which the denaturation process will occur is 80.degree. C. The temperature rise profile to the temperature L.sub.H should be as rapid as possible, generally 0.5 to 5 minutes, more preferably 1-3 minutes, to save time in the overall completion time of one cycle.
Of course, before all this may happen, the user must enter the checkpoint data. The steps to prompt the user for the checkpoints, to store the data so entered, and to retrieve it sequentially for calculation of set points are conventional and are not critical to the process, so they are not shown.
The amplification process of these empirical time embodiments involves a high-temperature incubation period for a user-defined, empirically determined time from start of heating to end of incubation. For implementation of the incubation, the computer starts a clock in step 84 and times the elapsed time from the start of heating toward temperature level L.sub.H and compares the elapsed time to a high-temperature incubation time, T.sub.H, entered by the user as symbolized by step 86. In the preferred embodiments, the incubation time variable may be set at any desired non-empirical value by the user in real time.
In other embodiments, the time T.sub.H (heating and high temperature incubation time) may be a fixed time which is experimentally determined and then "burned" into a ROM for permanent storage. In some embodiments, the CPU 20 may monitor the temperature of the heat exchanger 10 such as by use of the temperature sensor 80 shown attached to heat exchanger 10 in FIG. 1 and coupled to the CPU 20 through a line 81, and begin timing the high temperature incubation period when plate 1 reaches the temperature of temperature variable L.sub.H.
In the embodiment of FIG. 6, the user sets variable T.sub.H at a time which is empirically established to include the time it takes plate 1 to reach the desired temperature L.sub.H plus the desired time for high-temperature incubation at temperature L.sub.H. In embodiments where the computer starts tracking elapsed time only when the desired temperature L.sub.H is reached, i.e., where a temperature sensor 80 is used, the variable T.sub.H may be set by the user at the amount of time desired for high-temperature incubation at temperature L.sub.H without regard for the amount of time it takes for plate 1 to reach temperature L.sub.H. In the preferred embodiment, temperature L.sub.H is fixed at 90.degree.-100.degree. C. In both these embodiments, as will be appreciated, the time T.sub.H as described is a function of the time for which the container holding the reaction mixture is to be maintained at one temperature.
When the elapsed time at temperature L.sub.H equals the desired incubation time as determined by step 88, the CPU 20 sends the proper command to the heating and cooling apparatus to cause plate 1 to be cooled toward a low temperature incubation temperature LL set by the user. This is symbolized by step 90. Step 90 represents the transmission by the CPU 20 of a command, in the case of the embodiments of FIG. 2, to the fluid control multiplexer 46 to select the tubes 52 and 54 to couple to the tubes 42 and 44 such that fluid at the temperature of low-temperature fluid reservoir 18, set at LL by the user manually, begins to flow through the heat exchanger 10. In other embodiments, the CPU 20 may simply send a command to the heating and cooling apparatus to turn on an electrically driven refrigeration unit thermally coupled to plate 1, such as the Peltier heat pump 12. The range of chill-down rates from the high temperature to the low temperature which may be successfully used is governed by a balance of considerations. A very rapid chill-down, such as by using dry ice to bring the temperature of the reaction chamber down immediately, will inhibit or stop the amplification process. On the other hand, slow chill-down will lengthen the overall completion time of one cycle. Preferably, the chill-down rate will range from about 0.5 to 5 minutes, preferably in the range from 1 to 3 minutes. In the preferred embodiment, a fixed temperature within the range of from about 35.degree. to 60.degree.C. is set by the user by manual adjustment of low-temperature fluid reservoir 18 to maintain this temperature in the case of the embodiment of FIG. 2. In the case of the embodiment of FIG. 1, the CPU 20 will establish the proper direction of current flow and duty cycle based upon the user entered data for L.sub.L. The duty cycle may be based upon user-defined data for the particular leg or may be fixed in either type embodiment. The temperature range of from about 35.degree. to 60.degree. C. is the optimum temperature for the thermostable enzyme used in the amplification protocol. The broad range of temperatures at which the amplification protocol can be successfully performed is about 30.degree.-35.degree. to 105.degree. C.
The next step is symbolized by step 92 and represents the process of measuring the elapsed time and comparing it to the user-defined low temperature incubation time T.sub.L. The optimum time it takes to reach temperature L.sub.L is not exactly known, but approximately 1-3 minutes is known to be effective. In the empirical embodiments, the CPU 20 does not monitor the temperature of plate 1; it only keeps track of the elapsed time since the command was issued to chill plate 1. The user must empirically determine how long it takes to reduce the temperature of plate 1 to temperature L.sub.L. The CPU 20 in step 92 constantly compares the actual elapsed time to the user-defined time T.sub.L. When the required time has passed, processing proceeds to step 94.
Step 94 symbolizes the process of monitoring for completion of the low-temperature incubation. In some embodiments, the computer CPU 20 begins tracking elapsed time when temperature L.sub.L is reached. Step 94 represents the process of the computer comparing the actual elapsed time to a low-temperature incubation time, user-defined variable T.sub.L. In some embodiments, this variable is a real time, user-defined time stored in the memory of the computer, while in other embodiments, the time T.sub.L is fixed and permanently stored after being empirically determined.
As soon as the elapsed time equals the desired low-temperature incubation time T.sub.L, step 94 causes processing to proceed to a step 96, which increments a software cycle counter to mark the end of the first cycle. If the actual elapsed time does not equal the time T.sub.L, processing proceeds on line 98 to step 92 for another comparison of elapsed time to desired time T.sub.L. After step 96, the CPU 20 proceeds to step 100.
Step 100 and step 102 represent the process of comparison of the cycle count to a user-defined variable in memory representing the desired number of cycles. In some embodiments, the desired number of cycles is a fixed number, but in the preferred embodiment, the desired number of cycles is a user-defined number. This gives the user the flexibility to vary the number of cycles of amplification performed to account for the differing efficiencies of amplification of different nucleic acid sequences, as described further below. If the cycle count does not match the desired number of cycles, processing proceeds via line 104 to step 106 to reset the elapsed time clock, and from there processing proceeds to step 82 via line 108 where another cycle is begun. If the desired number of cycles has been performed, then processing proceeds to step 108. There it is determined whether the user desires to run another temperature profile stored in another "file" or database. Every temperature profile entered by the user has a link data field in which there is stored the file identification of the next file or temperature profile to be run, if any. The contents of this link field are read in step 108. If the user has made no entry to the link field, then processing proceeds to step 110, and a finished message is displayed. If step 108 finds a file number in the link field, then processing proceeds to step 112. This step resets the elapsed time clock, and retrieves the first checkpoint from the new file. Processing then proceeds, starting at step 82, to run the temperature profile determined by the checkpoints in the new file.
The control process of FIG. 6 shows only two checkpoints for the temperature profile. In other embodiments, a greater number of checkpoints may be used so long as there is a generally high temperature incubation and a generally low temperature incubation at the proper temperatures for sufficient times.
In the preferred non-empirical "closed loop" embodiments running the process shown in FIG. 7, the CPU 20 in step 81 starts the heating for leg 1 for the user-defined temperature profile at a default rate and starts the clock in step 83. The CPU 20 then computes a set point in step 85 as a target temperature and continuously monitors the temperature of plate 1 in step 87 and compares it to the set point on the user-defined temperature profile. Step 85 periodically updates the set point by computing the slope of the temperature profile between user-defined checkpoints and calculating the new set point based upon the slope and elapsed time at the time of the calculation. An error signal based on the comparison can be generated by the CPU 20 in step 89. This error signal is then converted to the proper control signal to control the heating and cooling apparatus in step 91. In the case of a solid state heat pump, the error signal is used to change the duty cycle. The updated control signal is then output on the line 56 to cause the heating and cooling apparatus to adjust the reaction chamber temperature. If plate 1 became hotter than the desired profile for a particular set point, then the cold fluid would be switched on to cool it in the embodiment of FIG. 2. In the case of the embodiment of FIG. 1, the direction of current flow through the solid state heat pump could be reduced or the "on" time of the heat pulse duty cycle could be reduced to reduce the error signal magnitude toward zero.
In the preferred embodiment control process of FIG. 7, the CPU 20 begins timing the elapsed time at the same time the command is sent to the temperature control apparatus to begin heating plate 1 to the high temperature incubation level in step 81. After step 91 (or step 89 if no error is present) is performed in FIG. 7, step 93 is performed to compare the actual elapsed time to the user-defined time stored in memory at which the next checkpoint shall have been reached. If the elapsed time is equal to or greater than the checkpoint time, processing proceeds to step 95 to retrieve the time and temperature data for the next checkpoint.
If the elapsed time is less than the time to the next checkpoint, processing returns on line 97 to step 87 on FIG. 7. The next set point is then calculated, and processing continues as described above.
The error signal computation of step 89 is done using any known proportional control algorithm. Such algorithms are well known and are described in Shinskey, Process Control Systems, 2d ed., Chapter 1 (McGraw Hill 1979) ISBN 0-07-056891x, which is hereby incorporated by reference.
After retrieval of the time and temperature data for the next checkpoint, the CPU determines in step 99 whether the complete temperature profile has been processed. If the cycle has not been completed, processing returns on line 97 to step 87 to compute the next set point. Processing then continues from step 87 as defined above.
If the temperature profile has been completed, then step 101 is performed to increment the cycle counter (a software counter) to indicate that one complete cycle through the temperature profile has been completed. Next, the CPU 20 retrieves from memory the value from a data field in the database indicating the desired number of cycles through the particular temperature profile just completed. This is symbolized by step 103. This value is retrieved from a database that is filled with the checkpoint data and other information supplied by the user via the user interface 22 in FIGS. 1 and 2 and stored in RAM 24. In step 105, the number of cycles completed is compared to the user-defined desired number of cycles.
If the desired number of cycles have not been completed, then processing returns to step 81 on line 107. The first checkpoint in the same profile is then retrieved, and the processing of the same checkpoints in the current temperature profile starts over again as described above.
If step 305 indicates that the desired number of cycles through the temperature profile have been completed, then step 109 is performed to determine file linkage. Some users may wish to run one temperature profile for some number of cycles, x, and then run a different temperature profile for a different number of cycles, y, and so on for several different temperature profiles. Each temperature profile database is given a file identification number, and each file has a link field in the database for that profile. The content of this link field is retrieved in step 109 and is the file number of the next temperature profile to be performed, i.e., the next file to be "run". If the contents of this link field are zero or some other predetermined code, then no linking is to occur and processing stops with an indication on the display that such is the case. If there is a linkage, step 111 is performed to retrieve the first checkpoint of the new profile and processing continues from step 81 as described above. The linking process is repeated at the end of the next temperature profile and the next until no linking address is found. Processing is then complete.
Operation of Embodiments for Amplification with Liquid Handling Capability
Referring to FIG. 8, there is shown a general block diagram of a machine which can perform the PCR DNA or RNA amplification process. The starting materials comprised of the DNA or RNA to be amplified and the necessary reagents are initially loaded into a reaction well 40A in plate 1. Plate 1 supports the reaction well 40A which may be a recess machined into the plate, but preferably is a plastic container which holds the fluids involved in the reaction and which sits in a recess formed in plate 1. In the preferred embodiment, plate 1 is an aluminum block with a plurality of recesses formed therein sized to allow 0.5 ml (milliliter) Eppendorf tubes to fit therein.
The purpose of the tubes is to line the reaction well to separate the fluids from the walls of the recess in the plate 1 to avoid cross contamination when the same reaction well is used to amplify different nucleic acid sequences. The purpose of plate 1 is to support the tubes and to act as a heat exchanger to transfer thermal energy to and from the fluids stored in the tubes in the reaction wells such that the reaction components may be incubated at various temperatures at the appropriate times in the process.
To that end plate 1 must be structured in such a way that the fluids in the reaction wells such as the well 40A may be heated and cooled at the appropriate times in the process and for the appropriate duration. Any structure or method may be used to perform this heating and cooling function such as by electrical heating and refrigeration apparatus in or connected to plate 1. It is only necessary that whatever apparatus is used for this heating and cooling be capable of reaching and sustaining the temperatures involved, and that the apparatus for heating and cooling can achieve the required temperature versus time profile. One such electrically driven heating and cooling apparatus is Peltier heat pumps available from Materials Electronics Products Corporation in Trenton, N.J. Such heat pumps are comprised of N and P type bismuth telluride in the form of oriented polycrystalline ingots with the ends soldered to copper bus bars interfaced with ceramic plates. These heat pumps heat or cool by driving currents through them in particular, known ways. These semiconductors have been used in the prior art by Gilford Instruments Corporation to heat and cool cuvettes, and are available in wattage ranges including 150 watts. These devices are capable of cooling or heating a mass of material to which they are thermally coupled to temperatures in a range from -150 to +110 degrees centigrade. Such semiconductors could be thermally coupled in known ways to plates 1 and 2 or could be directly thermally coupled to the insert tubes or wells which are placed in the storage wells in plate 2 and the reaction wells in plate 1. Such semiconductors can be easily controlled to reach and maintain particular temperatures by modulating the currents which flow through them in accordance with the desired temperature level according to standard process control algorithms.
In a preferred embodiment, water baths which maintain reservoirs of fluids at constant temperatures are used, and plate 1 is an aluminum plate or some other metal with good heat conducting properties. Passageways are machined or molded into the metal through which heated or cooled fluids may be pumped. In a preferred embodiment of the machine, plate 1 has a fluid inlet coupled to a tube 42A and a fluid outlet coupled to a tube 44A. These two tubes are coupled to the outputs of a fluid multiplexer 46A. The fluid multiplexer has two pairs of inputs. One pair is coupled to high temperature fluid conveyance tubes 48A and 50A and the other pair is coupled to low temperature fluid conveyance tubes 52A and 54A. Each pair of inputs has one input channel and one output channel. For example, the first pair has its input channel coupled to tube 48A and its output channel coupled to tube 50A. Likewise, the output pair of the fluid multiplexer 46A has one output channel, coupled to the tube 42A and one input channel, coupled to the tube 44A. The purpose of the fluid multiplexer 46A is to selectively couple either the first input pair, tubes 48A and 50A, or the second input pair, tubes 52A and 54A, to the output pair in accordance with a select signal on a line 56A. If the first pair of inputs is selected, the tube 48A is coupled in fluid communication to the tube 42A through an internal fluid passage in the fluid multiplexer 46A. Likewise, the tube 50A is coupled to the tube 44A through an internal fluid channel in the fluid control multiplexer 46A. A similar connection occurs if the second pair of inputs is selected. In this manner, the temperature of the plate 1 and the fluids stored in the tubes in the reaction wells such as the well 40A may be controlled by the state of a TEMP SELECT signal on the conductor 56A. In the preferred embodiment, the fluid multiplexer 46A is implemented with four solenoid operated valves properly interconnected with the tubes 42A, 44A, 48A, 50A, 52A and 54A. However, any apparatus that can perform the fluid switching noted above will suffice. Indeed, if electrical heating and refrigeration apparatus is used in connection with controlling the temperature of plate 1, the need for the fluid multiplexer 46A is eliminated.
The heated and cooled fluid flowing in the tubes coupled to the fluid multiplexer 46A is pumped, by pump 200A, from a high temperature fluid reservoir 58A and a low temperature fluid reservoir 60A respectively. The purpose of these reservoirs is to maintain a volume of fluid such as water or antifreeze at a constant temperature. In a preferred embodiment, the high temperature fluid is maintained at a constant temperature of 98 degrees centigrade and the low temperature fluid is maintained at a constant temperature of 37 degrees centigrade. The water baths 58A and 60A are adjustable in terms of the temperatures at which they maintain their fluid reservoirs. Water bath 60A is preferably adjustable so as to be able to achieve a reservoir temperature anywhere in the range from -35 to +150 degrees centigrade. The water bath 60A preferably has a water capacity of 13 liters and a rapid chill down feature so as to have a cool down rate in excess of 100 degree Centigrade per minute. This helps minimize temperature stabilization time. Any type of fluid heating and cooling apparatus which can achieve and maintain such temperatures over the duration of the PCR amplification process will suffice for purposes of the invention. In the preferred embodiment, VWR 1135 and VWR 1155 water baths are used.
As is described in more detail below, these embodiments do not require a thermostable enzyme. Referring to FIG. 8, this enzyme is stored in a receptacle such as the receptacle 62A in plate 2. Plate 2 is also a heat exchanger structure with the same material and the same type of internal configuration as plate 1 serving the same purpose as plate 1, i.e., to maintain the enzyme stored in plate 2 at the temperature of the fluid pumped therethrough. In the preferred embodiment, plate 2 is maintained at a constant temperature of -1 degree centigrade by chilled fluid circulating therethrough from a fluid circuit comprised of an inlet tube 64A, an outlet tube 66A and a constant temperature regulating water bath 67A similar to water baths 58A and 60A. All the water baths have circulating pumps which circulate fluid from the reservoir through the inlet and outlet tubes and the plates 1 and 2. In some embodiments, the water baths 58A and 60A and 67A will have temperature control inputs which are coupled to control signal lines carrying signals which control the temperatures at which the water baths maintain the fluid in the various reservoirs.
The PCR protocol or sequence in these embodiments requires that at certain times in the cycles, an enzyme be added to the reaction well so that it can be incubated at a certain temperature with the nucleic acid sequence being amplified and the other reagents in the reaction well. It is the purpose of a liquid handler 68A to provide the apparatus needed to make the transfer of enzyme from plate 2 to plate 1. Many types of liquid handlers are known, and any machine which can move fluid at a controllable time in a controllable amount in a given range of small volumes with sufficient accuracy from a first receptacle to a second receptacle will suffice for purposes of practicing the invention. Typically, amounts of enzyme in the range of 5 microliters plus or minus 20% must be transferred from plate 2 to plate 1, so the liquid handler must be able to accurately handle fluid amounts in this range of volumes. The manner of movement of the enzyme from plate 2 to plate 1 is not critical to the invention, and any one of a number of known ways of moving fluid may be used.
The preferred method of liquid movement involves use of a movable pipette which can be dipped into the enzyme storage receptacle to aspirate an aliquot of enzyme and then moved over the reaction well to deposit the aspirated enzyme. One machine of this type which may be used as the liquid handler 68A of this invention is the PRO/PETTE.RTM. liquid handler available from Cetus Corporation in Emeryville, Calif. The preferred embodiment uses the PRO/PETTE.RTM. machine for the liquid handler 68A. Another machine of this type which may be used as the liquid handler 68A of this invention is the PRO/GROUP.RTM. liquid handler also available from Cetus Corporation in Emeryville, Calif. Both these machines have microprocessors in them which drive a collection of stepper motors which move the various elements of the machine to allow an enzyme transfer from plate 2 to plate 1. The microprocessor of the PRO/PETTE.RTM. machine should be programmed with the PRO/PETTE EXPRESS.RTM. software with the plate to plate transfer file to operate satisfactorily as the liquid handler 68A. This software is available from Cetus Corporation, and is well known. The source code needed to modify the PRO/PETTE EXPRESS.RTM. software to cause the PRO/PETTE.RTM. liquid handler to run the PCR amplification protocol is attached hereto as microfiche Appendix A. The actual object code of the PRO/PETTE EXPRESS.RTM. software as modified to run the PCR amplification protocol is attached hereto as microfiche Appendix B. The microprocessor of the PRO/GROUP.RTM. liquid handler comes programmed with modified PRO/PETTE.RTM. software which includes all the routines or "files" of the PRO/PETTE EXPRESS.RTM. software plus some new files which do not exist in the PRO/PETTE EXPRESS.RTM. software, and which are not necessary to run the PCR protocol.
To run the PCR protocol on either the PRO/PETTE.RTM. or PRO/GROUP.RTM. liquid handlers, the two files of microfiche Appendix A plus the data structures listed there must be added to the PRO/PETTE EXPRESS.RTM. software. The combined software plus the Cetus Real Time Nucleus, and the motor controller code and hand held controller code for the particular machine selected must then be loaded into the program memory of the machine. Microfiche Appendix A is the source code for the PRO/PETTE.RTM. machine and calls the standard PRO/PETTE.RTM. routines for basic functions such as moving the bed and movable head. Those skilled in the art will appreciate that the source code of microfiche Appendix A may need to be modified somewhat to allow it to work properly with the PRO/GROUP.RTM. machines. The software for the PRO/GROUP.RTM. machine's motor controller chips, hand held controller microprocessor and Cetus Real Time Nucleus operating system is given in the remaining microfiche appendices.
If another liquid handler mechanism without an internal computer is used as the liquid handler 68A, a computer 70A having a control program stored in program memory 72A is used to control it. The computer 70A may be any general purpose computer or microprocessor which is capable of generating the proper control signals which are necessary to cause the liquid handler 68A to transfer the proper amount of enzyme from plate 2 to plate 1 at the proper time. There must also be the proper interface circuitry in the computer to convert the control signal from the computer to the proper type and amplitude of signal to cause the liquid handler 68A to properly carry out the transfer. The computer 70A must also be able to generate a temperature control signal to cause the temperature of plate 1 to be varied between the various temperatures needed in the process, and must be able to control duration and starting time of each incubation interval in the PCR amplification process.
The program stored in the program memory 72A will vary depending upon what type of heating and cooling apparatus is used to control the temperature of plate 1 and the type of liquid handler 68A used in the system. Certain criteria must be met, however, to cause the system to successfully carry out the amplification protocol. The process which the machine must perform is given in flow chart format in FIG. 9.
The amplification cycle of FIG. 9 starts at block 74A with with a command from the user to start the amplification processing. Prior to this time the user must have loaded the proper enzyme into the storage wells in plate 2 and the nucleic acid sequence to be amplified plus the proper reagents in the tubes must be stored in the reaction wells in plate 1. In some embodiments, the wells in plates 1 and 2 may be loaded with the proper starting materials automatically by the liquid handler under the control of the computer 70A.
Upon receiving the start command, the computer 70A in a step 76A issues the proper signal on the temperature select line 56A to cause the temperature control apparatus for plate 1 to heat plate 1 to a high temperature equal to temperature variable T1. In some embodiments, temperature variable T1 will not be a variable but will be a constant fixed at the temperature of the water bath which the user will manually set. In other embodiments, the variable will be user defined and the computer 70A will monitor the temperature of plate 1 and issue the proper command signal to the temperature control apparatus to cause it to heat plate 1 until the desired temperature is reached and then will issue the proper commands to the temperature control apparatus to cause the desired temperature to be maintained. In a preferred embodiment, a single fixed temperature water bath is used where the user sets the temperature of the bath. In this embodiment, the step 76A is comprised of a command on the line 56A to the fluid control multiplexer 46A to select tubes 48A and 50A for coupling to the tubes 42A and 44A. No monitoring of the temperature of plate 1 is done by the computer 70A in a preferred embodiment. However, in some embodiments, the temperature of plate 1 is monitored by the computer and an error signal is generated to control the temperature of plate 1 according to a user defined time versus temperature profile.
The temperature of plate 1 during this high temperature incubation should be maintained at 95 degrees centigrade plus or minus 3 degrees centigrade. The applicants believe that the process will occur at 90 degrees centigrade. The temperature rise profile to the temperature T1 should be as rapid as possible to save time in the overall completion time of one cycle.
The amplification process involves a high temperature incubation period. To implement the incubation, the computer times the elapsed time at the high temperature and compares the elapsed time to a high temperature incubation variable A as symbolized by step 78A. In the preferred embodiment, the incubation time variable may be set at any desired value by the user. In other embodiments, it may be a fixed time. In some embodiments, the computer 70A may monitor the temperature of plate 1 such as by use of a temperature sensor 79A shown attached to plate 1 in FIG. 8 and coupled to the computer through a line 81A, and begin timing the incubation period when plate 1 reaches the temperature of temperature variable T1.
In other embodiments such as that shown in FIG. 13 running the process shown in FIG. 14, the computer may continuously monitor the temperature of plate 1 and compare it to a user defined temperature profile. An error signal based on the comparison can be generated by the computer and interface circuitry (lumped together in box 70A in FIG. 13) on the line 56A to cause the fluid control multiplexer 46A (FIG. 8) to switch either the hot or cold fluid flow into the fluid passageways of plate 1 to control the temperature of the plate according to the profile if the heating and cooling apparatus of FIG. 8 is being used. That is, if plate 1 became hotter than the desired profile, then the cold fluid would be switched on to cool it. Conversely, the hot fluid would be switched on if plate 1 became colder than the desired temperature profile. Of course, the hot and cold fluid reservoirs and the fluid control multiplexer 46A could be dispensed with and the error signal on line 56A could be coupled to a heat pump driver 57A which in turn drives a thermoelectric heat pump such as a Peltier heat pump 59A as shown in FIG. 13. The amplification protocol the embodiment of FIG. 13 implements is shown in FIG. 14. The protocol of FIG. 14 is the same as that of FIG. 9 except that steps 77A, 83A, and 87A are inserted where shown to monitor the temperature sensor 79A and generate the error signal on line 56A to cause the heat pump driver 57A to control the heat pump 59A so as to maintain plate 1 on the desired temperature profile at each point in the elapsed time for the heat up and cool down cycles and the high temperature and the low temperature incubations respectively.
In a preferred embodiment, the computer begins timing the elapsed time at the same time the command is sent to the temperature control apparatus to begin heating plate 1 to the high temperature incubation level. In a preferred embodiment of FIG. 8, the user sets variable A at a time which is empirically established to include the time it takes plate 1 to reach the desired temperature plus the desired time for high temperature incubation. In embodiments where the computer starts tracking elapsed time only when the desired temperature is reached, the variable A may be set by the user at the amount of time desired for high temperature incubation without regard for the amount of time it takes for plate 1 to reach temperature T1. In a preferred embodiment, temperature T1 is fixed at 95 degrees centigrade.
When the elapsed time at temperature T1 equals the desired incubation time, the computer 70A sends the proper command to the heating and cooling apparatus to cause plate 1 to be cooled toward a temperature T2. This is symbolized by step 80A. In a preferred embodiment a fixed temperature of 37 degrees centigrade is set by the user by manual adjustment of low temperature fluid reservoir 60A to maintain this temperature. The applicants believe that 37 degrees centigrade is the optimum temperature for the particular enzyme used in the amplification protocol of example 4. Step 80A represents, in a preferred embodiment, the transmission by the computer 70A of a command to the fluid control multiplexer to select the tubes 52A and 54A to couple to the tubes 42A and 44A such that fluid at the temperature of low temperature fluid reservoir 60A, set at T2 by the user manually, begins to flow through plate 1. In other embodiments, the computer 70A may simply send a command to the heating and cooling apparatus to turn on an electrically driven refrigeration unit thermally coupled to plate 1. The applicants do not presently know the range of chill down rates from the high temperature to the low temperature which may be successfully used, but it is believed that a very rapid chill down such as by using dry ice to bring the temperature of the reaction chamber down immediately will inhibit or stop the PCR amplification process.
The next step is symbolized by step 82A and represents the process of measuring the elapsed time to bring plate 1 to temperature T2. The optimum time it takes to reach temperature T2 is not exactly known, but approximately three minutes is known to be effective. In a preferred embodiment, the computer 70A does not monitor the temperature of plate 1; it only keeps track of the elapsed time since the command was issued to connect the low temperature circulating fluid to plate 1. The user must empirically determine how long it takes to get the temperature of plate 1 down to temperature T2 or 37 degrees centigrade in a preferred embodiment. The computer 70A constantly compares the elapsed time to the user defined time. When the required time has passed, processing proceeds to step 84A. In other embodiments, the computer monitors the temperature of plate 1 and compares it to the temperature variable T2 which is set by the user. When temperature T2 is reached, processing proceeds to step 84A.
Step 84A represents the issuance of the proper commands to the liquid handler 68A to cause it to transfer an aliquot of enzyme from plate 2 to plate 1. In the preferred embodiment, the amount of enzyme which is transferred is user definable and varies from 5 microliters down to the minimum amount which the liquid handler can reliably measure and transfer. In the preferred embodiment, step 84A represents the steps of issuing the proper stepper motor commands in the PRO/GROUP.RTM. machine to cause it to pick up a row of disposable pipette tips and to make the transfer. The detailed steps of the transfer process will be given later herein.
After the transfer is complete a low temperature incubation is performed to complete the cycle as symbolized by the steps 86A and 88A. Step 86A symbolizes the process carried out by the computer of continuing to issue the proper command to cause plate 1 to continue to be cooled and maintained at low temperature T2. In some embodiments, this involves continually monitoring the temperature of plate 1 and issuing the proper commands to control the heating and cooling apparatus to maintain plate 1 at temperature T2. In a preferred embodiment, step 86A symbolizes the process of causing the fluid control multiplexer to continue to select tubes 52A and 54A for connection to tubes 42A and 44A.
Step 88A symbolizes the process of monitoring for completion of the low temperature incubation. In the preferred embodiment, the computer 70A begins tracking elapsed time at temperature T2 when the liquid transfer of step 84A is completed. Step 88A represents the process of the computer comparing the elapsed time to a low temperature incubation time variable C. In some embodiments, this variable is actually a fixed time stored in the memory of the computer. In the preferred embodiment, the variable C is user definable, and can be changed from one run to the next depending upon the user's wishes or needs.
As soon as the elapsed time equals the desired low temperature incubation time, processing proceeds to a step 90A which marks the end of the first cycle. In step 90A, the computer 70A increments a cycle count that it keeps in memory, and processing proceeds to step 92A.
Step 92A represents the process of comparison of the cycle count to a variable D in memory representing the desired number of cycles, i.e., the number of times the steps 76A through 88A are to be performed. In some embodiments, the variable D is a fixed number, but in the preferred embodiment D is a user definable number. This gives the user the flexibility to vary the number of cycles of amplification performed to account for the differing efficiencies of amplification of different DNA or RNA sequences. If the cycle count matches the desired number, processing proceeds to step 94A and the amplification process is complete. If not, processing proceeds to step 76A, and the next cycle is started immediately.
The Liquid Handler Apparatus
Referring to FIG. 10, there is shown an overall physical perspective view of the mechanical layout of one type of liquid handler which may be used to practice the invention. FIG. 10 represents a PRO/GROUP.RTM. machine, although a PRO/PETTE.RTM. machine will also work. In application of the PRO/GROUP.RTM. machine to perform the amplification protocol, many of its capabilities are not used. The machine includes several microprocessors including a microprocessor that performs bar code reading, a microprocessor which controls the user interface, microprocessors which are specially programmed to control the various stepper motors in the system and a central microprocessor which runs the main program and which communicates with all the other programs. The software which these various microprocessors run to perform all the tasks for which the PRO/GROUP.RTM. is programmed is included herewith in the microfiche appendices attached hereto starting with microfiche Appendix C and following in Intel hex code. All of these microfiche appendices are labeled as to which microprocessors each appendix pertains to. As noted above, the PRO/GROUP.RTM. machine is known and publicly available, and a description of this machine is made here only for completeness.
Another machine, the Cetus PRO/PETTE.RTM. liquid handler, which is described in U.S. Pat. No. 4,478,094, may also be used as the liquid handler 68A in FIG. 8, and is well known to those skilled in the art. Both the PRO/PETTE.RTM. and the PRO/GROUP.RTM. machine main microprocessors run programs written in the "C" high level language, and the various liquid handling routines which each machine performs are coded in "files". These files call upon various functional routines which do standard "building block" functions such as getting tips out of their storage positions, moving the multichannel head up or down, moving the plungers up or down to aspirate or deposit liquid using the pipette's, moving the table, and putting the tips back into their storage positions. As noted earlier herein, to run the amplification protocol on either of these machines requires that two new files and their associated data structures be programmed into the machine. These two new files and their associated data structures are included herewith as microfiche Appendix A. Microfiche Appendix A was written for the PRO/PETTE.RTM. machine, but can be adapted by those skilled in the art to also run on the PRO/GROUP.RTM. machine with little or no modification by adding the data structures given in microfiche Appendix A and adding the two files in object code format and insuring that the "building block" routines called in "seq-pcr" "file" or sequence have the same names and that the "seq-pcr" routine looks for them at the proper locations in memory. If a PRO/PETTE.RTM. or PRO/GROUP.RTM. machine is used for the liquid handler 68A, there is no need for a separate computer 70A or program memory 72A since these functions are implemented by the main microprocessor in the liquid handler.
Alternatively, those skilled in the art can use a different liquid handler 68A and write their own program to implement the process shown in the flow charts herein, or use a PRO/GROUP.RTM. machine and write an entirely new program to implement the detailed flow chart given below for the movements involved in the liquid handling steps. Such a program could be written by those skilled in the art easily given the description of the process herein.
FIG. 11 is a block diagram of the electrical control apparatus of the PRO/GROUP.RTM. liquid handler that drives the machine. Referring jointly to FIGS. 10 and 11 will give an integrated picture of the liquid handling machine's structure. A carrousel 120A stores a plurality of test tubes 122A which store tissue samples or chemicals or solutions to be assayed. The test tubes are shown as having bar codes 121A thereon. The actual positions of these bar codes are above the upper surface of the test tubes so that they can be read while the tubes are in their stored positions. Immediately radially behind each test tube is a storage position for a long pipette tip in the form of a hole in the carrousel in which a pipette tip rests such as the pipette 124A. The pipette tips have long projecting tips that can reach the bottom of the test tubes to extract tissue samples or chemicals from the bottom of the tubes. There is one tip stored for each test tube so that cross contamination will not occur as each tip is used with its particular test tube only.
The carrousel is moved by a stepper motor (not shown in FIG. 10) #1 in FIG. 11. Motor 1 moves the carrousel through a belt drive mechanism (not shown), but other drive mechanisms would work also such as direct drive or chain drive. The carrousel is moved so as to place one and only one test tube at any given time in an "active" position under an x-y head 128A. The x-y head is shown in its left position in preparation for moving its long pipette tip down into the test tube in the active position below the tip 130A. The x-y head has another position further left wherein a tip holder (not shown) is aligned directly over a projecting end of the pipette tip stored behind the test tube in the active position. The tip holder has an outside diameter which is matched to the inside diameter of the long pipette tip ends protecting from the pipette storage positions such that the tips can be picked up when the head is lowered such that the tip holder engages the tip.
The x-y head 128A is part of an integrated transfer head 132A which combines several liquid handling apparatus in one small space and shares the function of various drive motors among the various head units comprising the whole. The entire head 132A moves vertically (along the Z axis in FIG. 10) up and down on tracks (not shown) under the control of a head vertical motion motor #6 in FIG. 11 (not shown in FIG. 10) under the control of the main microprocessor 134A and a motor driver (not shown) in the interface circuit 136A. The x-y head 128A also moves horizontally (along the X axis in FIG. 10) under the control of the x-y head drive motor #5 in FIG. 11 (not shown in FIG. 10). The mechanical details of the transfer head 132A are contained in a copending patent application commonly assigned to the assignee of the present invention entitled "Liquid Manipulation Device and Method", filed Jul. 5, 1985, Ser. No. 752,449 which is hereby incorporated by reference.
In order to pick up a long tip such as the tip 130A, the motor #5 is commanded by the main microprocessor 134A and the interface board 136A to move the x-y head to the position where the tip holder is lined up with the tip stored behind the tube in the active position, and the motor #6 is commanded to move the entire head 132A down until the tip holder is seated in the projecting portion of the long tip stored in the tip holder position behind the active tube. The motor #6 is then commanded to lift the entire head to draw the entire tip out of the storage position. The tip can then be moved to any position along the X axis by motor #5.
The x-y head also has a movable piston (not shown) within the cylinder coupled to the pipette holder and tip. The piston can be moved up and down in the Z direction by a piston drive frame 138A which is connected to the piston, and which is driven by a piston drive motor #7 in FIG. 11 and shown at 140A in FIG. 10. This motor is connected by a worm gear (not shown) to the piston drive frame 138A such that rotation of the worm gear is translated into Z axis motion of the frame 138A.
The integrated head 132A is also comprised of a multichannel head 142A, a wash head 144A and a dispense manifold 146A.
The dispense manifold 146A is a multichannel liquid dispense manifold with multiple outlets 148A which can be lowered into wells to fill them with liquids pumped into the manifold 146A by a peristaltic pump 150A through a section of flexible hose 152A. The input of the pump is coupled through another hose 154A to a reservoir of solution such as saline solution. In the preferred embodiment, the dispense manifold has the same number of outlets 148A as there are wells in mixing plates 156A, 158A and a diluent tray 160A and a reagent tray 162A and has the same center to center spacing for the outlets 148A as the wells in the trays have. The plates 156A and 158A are the heat exchanger blocks designated plate 1 and plate 2 in the preferred embodiment, and are connected to the fluid control multiplexer 46A and to the constant temperature fluid reservoirs by the tubes 44A and 42A and the tubes 64A and 66A, respectively. In the preferred embodiment, the diluent tray 160A and the reagent tray 162A are replaced by a single tip storage tray with wells for storage of multiple rows of pipette tips. Each well is completely enclosed in the preferred embodiment such that when liquid clings to the tip there is no chance of the liquid being thrown, blown or flipped off the tip when the tip is ejected because of the physical barrier surrounding each tip. This is another measure taken to prevent cross contamination.
Although the liquid handler of FIG. 10 has the capability of reading bar codes on the plates and tubes, the amplification protocol does not utilize this capability.
The wash head is a multichannel head for filling the wells in the various trays with wash solutions, preventing overfill conditions and for emptying the wells. Each well filling position, and there are a plurality of such positions, has an empty and overfill cannula which is connected to an evacuated manifold to empty wells, and a fill cannula which is connected to a manifold which is supplied by wash liquid under pressure from a peristaltic pump 164A through a flexible tube 166A. The input to the pump 164A is connected through a flexible tube 168A to a wash solution reservoir. The wash head 144A is coupled to the integrated head 132A by a mechanism (not shown) such that it can be lowered up and down independently of any movement of the entire head. There is a separate wash head movement motor, motor #11 in FIG. 11 which implements the independent wash head movement, and a solenoid operated valve 172A, #12 in FIG. 11.
The pumps 150A and 164A are driven by pump motors #3 and #4 respectively in FIG. 11 under control of the main microprocessor 134A and motor drive controllers (not shown) in the interface 136A.
The multichannel head 142A consists of a plurality of pipette tip supports which are equal in number and have the same center to center spacing as the wells in the plates 156A, 158A, 160A and 162A under the head. Each tip support, as in the case of the long tips picked up by the x-y head, is sized so as to fit into the projecting end of a short tip stored in a storage position in the plate 162A beneath the head. The manner of picking up the tips is the same as in the case of the x-y head but there is no need to move the multichannel head 142A in the X direction. This is because the plate 62A is in a registered position on a bed 174A such that the tip supports are exactly lined up with the center lines of the tips stored in the storage positions in the plate 62A. The bed 174A is supported on rails (not shown) such that it can slide either way in the Y direction. The bed 174A is driven by a belt drive and a motor #2 in FIG. 11 (not shown in FIG. 10) to cause movement to any desired position on the Y axis. Such movements are made under control of the main microprocessor 134A and the motor controller for motor #2 in the interface 136A. In other embodiments, the head 132A may be mounted on tracks and moved in the Y direction, and the bed 174A can be stationary. To pick up a short tip, the bed 174A is moved such that the short tips are lined up under the multichannel head tip supports and the integrated head 132A is lowered until the tip supports are seated in the short tip projecting portions. FIG. 10 shows the multichannel head with short tips in position on the tip supports. The multichannel head can move in the Z direction only under the control of motor #6 and the main microprocessor 134A.
There is a tip ejector plate (not shown) located at the bottom of the multichannel head 142A between the upper ends of the tips closest to the multichannel head and the bottom surface of the multichannel head. This plate can move up and down in the Z direction under control of two tip ejector solenoids 176A and 178A controlled by the computer and symbolized as solenoids #8 in FIG. 11. When these solenoids are activated, the tip ejector plate is driven down, and the tips are ejected. During this tip ejection action, the tip ejector plate travels a known distance, D, downward. The significance of this is as follows. In the preferred embodiment, the tips have ribs extending radially therefrom around the circumference of the tip at the end where the multichannel head engages the tip. These tips extend longitudinally down the tip for a short distance and stop. The ends of these ribs provide support points upon which the tip rests when it is in place in its storage container. In the preferred embodiment, after an enzyme transfer cycle when the tips are about to be ejected back into their storage wells, the multichannel head is lowered to a point such that the bottoms of the ribs are located a distance D above the top surface of the tip storage well upon which the ribs of the tips will eventually rest. The tip ejector plate is then operated such that the tips are driven down into solid contact with the tip storage tray. This prevents the tips from wobbling when they are ejected such that fluid clinging to the tip is discouraged from being thrown off. This minimizes the chances of cross contamination where multiple tips which are mapped to specific rows of nucleic acids and specific rows of enzymes are used. There is also a projection on the tip ejector plate to eject the long tip on the x-y head when it is moved to the extreme right position in the X direction (farthest from the origin).
There are two bar code read heads which cannot be seen in FIG. 10 and which serve to read bar codes on the test tubes and the mixing trays to provide identifying information to the host computer and supervisory microprocessor 134A regarding the samples or chemicals in the test tubes and the donors or chemicals present in the mix trays. These bar code readers are conventional and their details of structure and operation need not be given here.
There is a hollow cavity or cylinder in the x-y head which has a volume which changes with position of the piston drive frame 138A. The mechanical details of the x-y head 128A are known and available from Cetus Corporation in Emeryville, Calif. in certain models of the PRO/PETTE.RTM. liquid handler. This internal volume is coupled in any conventional way to a pressure transducer (not shown) by a flexible hose 180A which is long enough to not interfere with operation of the head 132A. Preferably the pressure transducer is mounted in the instrument cabinet 182A near the main microprocessor 134A and the interface 136A. This transducer is symbolized by the transducer #13 in FIG. 11.
FIG. 11 also includes a programmable read only memory (PROM) 184A and a random access memory (RAM) 186A. The PROM stores all the preprogrammed sequences of instructions, i.e., subroutines and "files", for various operations which cause the main microprocessor 134A to send the proper addresses, data and control signals on the busses 188A, 190A and 192A to the interface 136A to cause the peripheral devices and motors etc., #'s 1-13, to perform the proper movements in the proper sequence. The PROM also contains instructions to ask the user a series of initialization questions regarding the process parameters to be used for each process. The questions are asked through a series of displayed messages on the display of the user interface 194A. Default answers are stored in the PROM and any answers provided by the user through the keyboard on the user interface are read by the main microprocessor 134A and stored in a database for that particular file in an EEPROM 185A. The EEPROM 185A then stores the user supplied answers for a modified file as a database for that file along with the file number supplied by the user for that file and the routine in PROM 184A to which the data pertains. Thereafter, when the user requests that that file be run, the main microprocessor 134A accesses the database in EEPROM 185A and stores it in RAM 186A. When the computer needs to know how much liquid to draw, which wells to put it in etc., it accesses the particular process parameter it needs from RAM 186A when it reaches the particular point in the instruction sequence stored in PROM 184A that calls for the data. There is also a linking field stored in the database for each file which instructs the main microprocessor 134A which file, i.e., which address in the EEPROM 185A to start with in executing the next file stored in EEPROM 185A after completing execution of the file currently being processed. Only user modified files stored in EEPROM 185A can be linked. At the end of each subroutine in PROM 184A there is an instruction or set of instructions which cause the main microprocessor 134A to access the database for that file in EEPROM 185A and read the linking field. That field will contain the address of the starting point for the next sequence of instructions, i.e., the next file, to be run by the main microprocessor 134A from the EEPROM 185A. By changing the contents of the linking field in the database for each file, the user can put together long strings of files for execution. The user is asked at the end of each batch of file initialization questions whether he wants to link the file he his just customized to another file.
The interface 136A serves to connect the host computer to the bar code scanners through a UART 187A and to the motors through a plurality of single chip microprocessor motor controllers. The host microprocessor 134A, an Intel 8085 for which the software is included herewith as a microfiche appendix has data, address and control busses 190A, 188A, and 192A which are coupled to a UART 187A and a dual UART 189A. The two UART's convert the parallel data on the data bus 190A to serial data for communication to other devices in the interface and to a host CPU (not shown). The serial data from the UART 187A is coupled on line 191A to a set of Intel 8051 microprocessors which are programmed as motor controllers 193A. The program which customizes each general purpose Intel 8051 microprocessor to become a stepper motor controller (each controller is identical, and each controller can control 4 motors in the system) is attached hereto as a microfiche appendix.
To run the amplification sequence, one of the motor controller output pins is dedicated to controlling the fluid control multiplexer. This is shown as line 56A coupling the motor controllers 193A to a solenoid driver 57A. This solenoid driver may either drive the solenoids directly or may drive a relay which in turn controls the current flow through the solenoids which are used to implement the fluid control multiplexer 46A in FIG. 8.
Each microprocessor programmed with the code of microfiche Appendix C becomes a motor controller which can accept a predetermined set of motor control commands from the main microprocessor 134A to start and stop each motor it controls, tell each how many steps to move, and tell each the run rate. Each motor controller can also read the position of any motor under its control and report that information to the main microprocessor 134A. The microprocessor 134A sends these motor controllers commands which control the modes the motors operate in, indicate which motor is being addressed, and controls whether the motor is to be started, stopped, jogged or sent to its home position. Certain data bytes are sent to specify the start rate, the run rate, the jog rate, the acceleration rate and the maximum position limit to which the motor will be allowed to move. These data bytes are used to control the velocity profile for each movement of the motors for maximum accuracy in delivery quantities and position. Every start, jog and home command will also contain a destination word indicating the desired position to which the motor should move its driven part. There are also read commands so that the main microprocessor 134A can read the position of any given motor to determine the position of that motor's driven part.
The line 191A is also coupled to a bar code microprocessor 195A, the software for which is included herewith as a microfiche appendix. The bar code microprocessor 195A is coupled to the bar code read heads #'s 9 and 10, and interprets their signals. The mechanical details of the placement and apparatus for causing the bar code read heads to read the bar codes are conventional. The data derived from the bar code read heads is sent to the main microprocessor 134A via the line 191A and the UART 187A for storage in the RAM 186A.
The signals on the control bus 192A tell the various interface circuits whether the computer is reading or writing and other things about the status of the busses and the main microprocessor 134A. Each of the motor controllers, UART's and the A/D converter has a separate chip select input on the control bus 192A such that the microprocessor 134A can individually address each one of these devices alone while the other devices have their bus ports in the tri-state condition effectively isolating the desired device on the bus.
The motor controllers 193A also contain I/O pins which are connected to the tip eject solenoid #8 and to the wash head solenoid vacuum control valve. These pins have specific addresses, and when the host main microprocessor 134A wishes to activate one of the solenoids, it addresses the particular I/O pin and sends a data byte which changes the voltage level on the I/O pin to the proper level to activate the solenoid in the proper fashion.
In addition the interface 136A has an A/D converter 197A to convert the analog signal from a pressure transducer #13 to a digital signal which can be read by the main microprocessor 134A and put through a comparison routine. The purpose is to sense pressure rises in the pipette connected to the x-y head of greater than a certain amount. The A/D converter has a conversion ready interrupt line 199A which signals when the conversion is ready. This line is regularly polled by the microprocessor 134A, and when it signals the conversion is ready, the host computer reads the conversion data from the A/D converter and stores it for a comparison.
Alternatively, the pressure transducer interface circuitry can consist of any circuit which can detect a rise in the pressure in the chamber of the x-y pipette tip. One way of doing this is to set a known reference level and compare the signal from the transducer to the reference level. When the level is exceeded, an interrupt can be generated to signal the processor that the condition being watched for has occurred.
The UART 189A is coupled to a user interface 194A consisting of a display and keyboard through which the host main microprocessor 134A displays messages and queries to the user and reads the users responses on the keyboard. The manner of displaying and reading the queries is conventional. There is also a printer 101A which can be connected to the UART 189A to print the user defined files stored in EEPROM 185A.
The specific software sequence that the host microprocessor 134A runs to perform the amplification protocol is attached hereto in source code format as microfiche Appendix A, and starts at page 4 thereof as the "seq-pcr" sequence. Microfiche Appendix A, pages 1-3, also includes the data structures and text strings that need to be added to the PRO/GROUP.RTM. software attached hereto as the other microfiche appendixes to modify it to run the amplification protocol embodied in the software of microfiche Appendix A. The amplification process motor movement commands, display commands and solenoid valve control commands start with the statement at line 11 of page 4. The source code of the amplification sequence will be explained with reference to the flow diagram of FIG. 12 which is a PRO/GROUP.RTM. and PRO/PETTE.RTM. specific movement and command sequence to implement the amplification protocol.
The sequence starts with step 200A which constitutes a start command from the user interface terminal 194A after the user has answered a series of questions regarding the desired process parameters which are to control the various aspects of the process. The database of process parameters is built by the known PRO/PETTE.RTM. or PRO/GROUP.RTM. file editor. The database is stored in an array shown in microfiche Appendix A. The user is requested by the editor to supply a time in minutes and seconds for the high temperature incubation and a time for the low temperature chill down. The user is also asked to supply the volume desired for the enzyme transfer and the amount of enzyme to aspirate during the enzyme pick-up stage. The user is also asked to specify how much enzyme to aspirate and expel during the mixing stage and how much enzyme to dispense during the initial discharge of enzyme into the reaction chamber. Finally, the user is asked to specify the time for the post transfer incubation at low temperature, any rows to skip, the number of amplification cycles to perform and the speed of liquid transfer followed by the number of the next file to link to for further processing. All this activity is symbolized by the block 195A.
After the process parameters are defined and the array shown in microfiche Appendix A is filled in, the user is asked whether he or she wishes to run the amplification file, print the process parameters just defined or store the answers in memory for future use. This is symbolized by step 196A. If the answer is store or print, processing proceeds to the appropriate one of blocks 197A or 198A to carry out the appropriate action. If the answer is run, processing proceeds to step 200A and the amplification protocol is begun.
The first step is to home all the relevant stepper motors to a known home position as symbolized by step 202A. Next, the microprocessor checks the process parameter array to determine whether the high temperature incubation time is non-zero as symbolized by step 204A. If it is non-zero, processing proceeds to step 206A where the high temperature apparatus is switched on to begin heating plate 1 to the high temperature incubation temperature. The elapsed time from the time the high temperature mechanism is turned on is timed in step 208A and compared to the time in the process parameter array (hereafter the array). When the two times are equal, processing proceeds to step 210A where the time for chill down to the transfer temperature defined in the array is examined to determine if it is non-zero. If the answer in step 204A was that the high temperature incubation time was zero, processing proceeds directly to step 210A. Steps 204A to 208A are implemented by lines 31 through 34 on page 4 of microfiche Appendix A.
If the answer to the question of step 210A is that a non-zero chill down time is specified in the array, then processing proceeds to step 212A to switch on the low temperature mechanism. At this time, the system begins timing the elapsed time since the chill mechanism was turned on as symbolized by step 214A. When this time equals the chill down time specified in the array, processing proceeds to step 216A to begin the transfer of enzyme from plate 2 to plate 1. The chill down time specified in the array is preferably empirically determined to be the time it takes to chill plate 1 from 98 degrees centigrade to 37 degrees centigrade. Steps 210A through 214A are implemented by the code at lines 36 to 39. The steps 206A and 212A are implemented by the "mtr-cmd" statements at lines 33 and 37 respectively. The statement at line 33 clears one output bit on one motor controller chip which bit is coupled through suitable interface circuitry to the solenoid operated valves which are used to implement the fluid control multiplexer 46A of FIG. 8. Clearing this bit causes the heated fluid to be switched to a circulatory path through plate 1. The statement of line 37 sets the same bit which causes the solenoid operated valves to switch such that the chilled fluid is switched into a circulatory path which includes plate 1.
The first step in the transfer of enzyme is to pick up tips in step 216A. This is a known, standard PRO/PETTE.RTM. and PRO/GROUP.RTM. routine (known routines from these two machines will hereafter be referred to as standard routines and their details will not be given other than a short summary of what they do) which moves the bed 174A such that the multichannel head is aligned over the row of pipette tips stored in a tip storage tray in the position 162A. The integrated head 132A is then lowered until the nozzles of the multichannel head 142A engage the pipette tips with a press fit and the head is picked up to allow the tips to clear the storage block. The multichannel head 142A is modified for the amplification protocol in that only 6 channels, i.e., every other channel, are used because of the increased width of the plastic inserts in the reaction chambers. These inserts are wider than the wells in the plates normally used with the PRO/PETTE.RTM. and PRO/GROUP.RTM. machines, so every other channel is used. The process of step 216A is implemented in microfiche Appendix A by the statement at line 12 of page 5.
After the tips are picked up, the bed 174A is moved to put the proper row of the enzyme containing wells in plate 2 under the pipette tips as symbolized by step 218A on FIG. 12B. This is implemented by calling the standard routine move-m(TABLE . . . shown on line 14 of page 5 of microfiche Appendix A.) The row from which enzyme is picked up is alternated in cyclical fashion during each amplification cycle. This is implemented by lines 11-25 at page 4 of microfiche Appendix A.
Next, step 220A is performed to aspirate the amount of enzyme specified in the array from the appropriate well. To do this a call is made to the "move head" standard routine at line 14 at page 5 of microfiche Appendix A, and this is followed by a call to a standard aspirate routine which checks the array for the desired amount and orders the piston drive motor 140A to move the piston far enough to aspirate the desired amount of enzyme. After the enzyme is aspirated, another call to the "move head" standard routine is made to lift the tips up out of the enzyme far enough to clear the enzyme storage plate. The process of step 220A is implemented by the statements at lines 16 and 17 at page 5 of microfiche Appendix A.
The next step is to deposit the desired amount of enzyme into the plastic inserts in the row of reaction chambers in plate 1. This is symbolized by step 222A. This step calls the standard "move bed" routine to move the bed 174A to place the appropriate row of reaction chambers under the tips as implemented by line 17 at page 5 of microfiche Appendix A. The head 132A in FIG. 10 is then moved down to place the tips in the liquid in the plastic inserts in the reaction chambers as implemented by line 18 at page 5 of microfiche Appendix A. The standard expel routine is called at line 19 which checks the array for the desired amount of enzyme to deliver and orders the piston drive motor 140A to move the piston drive frame 138A and pistons far enough to expel the amount of enzyme specified by the user in the array.
Next in step 224A, the array is checked to determine if the user desires a mix sequence to be performed. This is implemented by line 21 at page 5 of microfiche Appendix A. If the answer is yes, the standard "aspirate" and "expel" routines are called alternately at lines 22 and 23 to aspirate the amount of enzyme specified in the "mix volume" entry in the array and to discharge it back into the chamber. This is repeated the number of times specified in the array. The last "expel" call causes the piston drive motor 140A to move the piston drive frame 138A down farther than necessary to expel the specified amount of enzyme. This is done to "blow out" the last drops of enzyme and reaction mix to prevent a drop from falling out of the pipette when the tips are moved back to their storage positions, possibly thereby causing cross-contamination. This is symbolized by step 228A and is implemented by the "putips" routine called at line 28 at page 5 of microfiche Appendix A. This routine is slightly modified for the amplification protocol however in that the tips are not ejected until the head is lowered to the point that the bottoms of the ribs on the tips are located a distance D above the top surface of the plate where D is equal to the distance that the tip ejector plate moves during the ejection motion. The tips are ejected into the row in the tip storage block which is mapped to the row of enzyme and the row of reaction chambers between which the enzyme aliquot was just transferred. In the preferred embodiment, each tip is completely surrounded by a physical barrier tip storage well to prevent cross contamination by splashing.
This completes the enzyme transfer for the first cycle. A step 230A then increments the tip pointer to the next tip row. There are plural rows of tips, enzyme storage wells and reaction chambers in the preferred embodiment. Each row of tips is mapped to a specific row of enzyme and a specific row of reaction chambers to prevent the tips in a particular row from ever touching nucleic acid from one row of reaction chambers and accidentally cross contaminating the nucleic acid in another row of reaction chambers by virtue of liquid clinging to pipette tips. The tips rows are mapped to particular enzyme rows because multiple transfers of enzyme are transferred between each row of enzyme and its assigned row of reaction chambers. Because of the multiple transfers, and because the liquid clings to the tips during each transfer, each row of enzyme becomes contaminated with the nucleic acid from its assigned row. If only one enzyme row were used for all reaction chamber rows, cross contamination could occur which could destroy the integrity of the amplification procedure. The amplification protocol is carried out on only one row of reaction chambers in plate 1 during any particular cycle. The increment tip pointer step 230A merely prepares the machine for the next cycle to pick up the appropriate row of tips which are used for processing the next row of reaction chambers to be processed. This step is implemented by lines 36 and 37 at page 5 of microfiche Appendix A.
Next, the computer checks the array to determine if the low temperature incubate time is non-zero as symbolized by step 232A. If it is, the computer begins timing the low temperature incubation elapsed time in step 234A. When the specified time has elapsed, processing proceeds to step 236A where the number of amplification cycles completed at that point is compared to the number of amplification cycles desired by the user. If the desired number have been completed, processing is done as symbolized by step 238A. If more cycles remain to be done, processing returns to step 200A on FIG. 12A.
Adaptation of the PRO/GROUP.RTM. or PRO/PETTE.RTM. Machines for Heat or Cool Steps During Other Assays
Heating and/or cooling steps are sometimes useful in assays to do such things as heat reagents or reaction mixes or cool the same. To carry out such an assay using the apparatus disclosed herein and the known PRO/GROUP.RTM. and PRO/PETTE.RTM. machines would require a simple modification of the programs stored in those machines. For example, to perform a heating or cooling step at any point in the blood grouping process carried out by the PRO/GROUP.RTM. machine as disclosed in the U.S. patent application identified above and incorporated herein by reference describing that machine and the blood grouping process performed by it, certain statements would have be added to the program run by the machine. Those statements are the motor command statements shown at lines 33 and/or 37 at page 5 of microfiche Appendix A. The statement at line 56 would be added at the appropriate place in the code implementing the step in the process where a heating step was desired, and the statement at line 60 would be added at the appropriate place in the code implementing a step in the process where a cooling step was to be performed. Another example of a process which could be performed to advantage using the heating and cooling steps of which the machine is capable is the process disclosed in U.S. Pat. No. 4,683,202 "Method for Detection of Polymorphic Restriction Sites and Nucleic Acid Sequences", which is hereby incorporated by reference.
Amplification Protocol
The amplification protocol automated by the present invention is a process for amplifying existing nucleic acid sequences using thermostable enzymes. The amplification process is disclosed and claimed in U.S. patent application Ser. No. 899,513 filed Aug. 22, 1986, now abandoned (Cetus Case 2177.3) filed concurrently herewith, wherein Cetus Corporation is the assignee, as in the present invention, entitled "Process for Amp-lifying, Detecting, and/or Cloning Nucleic Acid Sequences Using A Thermostable Enzyme." The disclosure for said application is herein incorporated by reference.
More specifically, the amplification method involves amplifying at least one specific nucleic acid sequence contained in a nucleic acid or a mixture of nucleic acids, wherein if the nucleic acid is double-stranded, it consists of two separated complementary strands of equal or unequal length, which process comprises:
(a) contacting each nucleic acid strand with four different nucleotide triphosphates and one oligonucleotide primer for each different specific sequence being amplified, wherein each primer is selected to be substantially complementary to different strands of each specific sequence, such that the extension product synthesized from one primer, when it is separated from its complement, can serve as a template for synthesis of the extension product of the other primer, said contacting being at a temperature which promotes hybridization of each primer to its complementary nucleic acid strand;
(b) contacting each nucleic acid strand, at the same time as or after step (a), with a thermostable enzyme which catalyzes combination of the nucleotide triphosphates to form primer extension products complementary to each strand of each nucleic acid;
(c) heating the mixture from step (b) for an effective time and at an effective temperature to promote the activity of the enzyme, and to synthesize, for each different sequence being amplified, an extension product of each primer which is complementary to each nucleic acid strand template, but not so high as to separate each extension product from its complementary strand template;
(d) heating the mixture from step (c) for an effective time and at an effective temperature to separate the primer extension products from the templates on which they were synthesized to produce single-stranded molecules, but not so high as to denature irreversibly the enzyme;
(e) cooling the mixture from step (d) for an effective time and to an effective temperature to promote hybridization of each primer to each of the single-stranded molecules produced in step (d); and
(f) heating the mixture from step (e) for an effective time and to an effective temperature to promote the activity of the enzyme and to synthesize, for each different sequence being amplified, an extension product of each primer which is complementary to each nucleic acid strand template produced in step (d), but not so high as to separate each extension product from its complementary strand template, wherein steps (e) and (f) may be carried out simultaneously or sequentially.
Steps (d)-(f) may be repeated until the desired level of sequence amplification is obtained.
The amplification method is useful not only for producing large amounts of an existing completely specified nucleic acid sequence, but also for producing nucleic acid sequences which are known to exist but are not completely specified. In either case an initial copy of the sequence to be amplified must be available, although it need not be pure or a discrete molecule.
The term "oligonucleotide" as used herein is defined as a molecule comprised of two or more deoxyribonucleotides or ribonucleotides, preferably more than three. Its exact size will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide. The oligonucleotide may be derived synthetically or by cloning.
The term "primer" as used herein refers to an oligonucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product which is complementary to a nucleic acid strand is induced, i.e., in the presence of four different nucleotide triphosphates and a thermostable enzyme at a suitable temperature and pH.
The primer is preferably single-stranded for maximum efficiency in amplification, but may alternatively be double-stranded. If double-stranded, the primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is an oligodeoxyribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of thermostable enzyme. The exact lengths of the primers will depend on many factors, including temperature, source of primer and use of the method. For example, depending on the complexity of the target sequence, the oligonucleotide primer typically contains 15-25 or more nucleotides, although it may contain more or fewer nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with template.
The primers herein are selected to be "substantially" complementary to the different strands of each specific sequence to be amplified. This means that the primers must be sufficiently complementary to hybridize with their respective strands. Therefore, the primer sequence need not reflect the exact sequence of the template. For example, a non-complementary nucleotide fragment may be attached to the 5 end of the primer, with the remainder of the primer sequence being complementary to the strand. Alternatively, non-complementary bases or longer sequences can be interspersed into the primer, provided that the primer sequence has sufficient complementarity with the sequence of the strand to be amplified to hybridize therewith and thereby form a template for synthesis of the extension product of the other primer. However, for detection purposes, particularly using labeled sequence-specific probes, the primers typically have exact complementarity to obtain the best results.
As used herein, the terms "restriction endonucleases" and "restriction enzymes" refer to bacterial enzymes each of which cut double-stranded DNA at or near a specific nucleotide sequence.
For embodiments employing liquid handling apparatus but not a thermostable enzyme, to the cooled mixture is added an appropriate agent for inducing or catalyzing the primer extension reaction (herein called "inducing agent"), and the reaction is allowed to occur under conditions known in the art. This synthesis reaction may occur at from room temperature up to a temperature above which the inducing agent no longer functions efficiently. Thus, for example, if DNA polymerase is used as inducing agent, the temperature is generally no greater than about 40.degree. C. Most conveniently the reaction occurs at approximately 37.degree. C.
The inducing agent may be any compound or system which will function to accomplish the synthesis of primer extension products, including enzymes. Suitable enzymes for this purpose include, for example, E. coli DNA polymerase I, Klenow fragment of E. coli DNA polymerase I, T4 DNA polymerase, other available DNA polymerases, reverse transcriptase, and other enzymes, including heat-stable enzymes, which will facilitate combination of the nucleotides in the proper manner to form the primer extension products which are complementary to each nucleic acid strand. Generally, the synthesis will be initiated at the 3' end of each primer and proceed in the 5' direction along the template strand, until synthesis terminates, producing molecules of different lengths. There may be inducing agents, however, which initiate synthesis at the 5' end and proceed in the other direction, using the same process as described above.
As used herein, the term "thermostable enzyme" refers to an enzyme which is stable to heat and is heat resistant and catalyzes (facilitates) combination of the nucleotides in the proper manner to form the primer extension products which are complementary to each i nucleic acid strand. Generally, the synthesis will be initiated at the 3 end of each primer and will proceed in the 5' direction along the template strand, until synthesis terminates, producing molecules of different lengths. There maybe thermostable enzymes, however, which initiate synthesis at the 5' end and proceed in the other direction, using the same process as described above.
The thermostable enzyme herein must satisfy a single criterion to be effective for the amplification reaction, i.e., the enzyme must not become irreversibly denatured (inactivated) when subjected to the elevated temperatures for the time necessary to effect denaturation of double-stranded nucleic acids. Irreversible denaturation for purposes herein refers to permanent and complete loss of enzymatic activity. The heating conditions necessary for denaturation will depend, e.g., on the buffer salt concentration and the length and nucleotide composition of the nucleic acids being denatured, but typically range from about 90.degree. to about 105.degree. C. for a time depending mainly on the temperature and the nucleic acid length, typically about 0.5 to four minutes. Higher temperatures may be tolerated as the buffer salt concentration and/or GC composition of the nucleic acid is increased. Preferably, the enzyme will not become irreversibly denatured at about 90.degree.-100.degree. C.
The thermostable enzyme herein preferably has an optimum temperature at which it functions which is higher than about 40.degree. C., which is the temperature below which hybridization of primer to template is promoted. The higher the temperature optimum for the enzyme, the greater the specificity and/or selectivity of the primer-directed extension process. However, enzymes which are active below 40.degree. C., e.g., at 37.degree. C., are also within the scope of this invention provided they are heat-stable. Preferably, the optimum temperature ranges from about 50.degree. to 80.degree. C., more preferably 60.degree.-80.degree. C.
Examples of enzymes which have been reported in the literature as being resistant to heat include heat-stable polymerases, such as, e.g., polymerases extracted from the thermophilic bacteria Thermus flavus, Thermus tuber, Thermus thermophilus, Bacillus stearothermophilus (which has a somewhat lower temperature optimum than the others listed), Thermus aquaticus, Thermus lacteus, Thermus rubens, and Methanothermus fervidus.
The preferred thermostable enzyme herein is a DNA polymerase isolated from Themus aquaticus, strain YT-1, and purified as described in U.S. application Ser. No. 899,241, filed Aug. 22, 1986 now abandoned (Cetus Docket 2303), entitled "Purified Thermostable Enzyme," the disclosure of which is incorporated herein by reference. Briefly, Thermus aquaticus cells are grown and the polymerase is isolated and purified from the crude extract using the first five steps indicated by Kaledin et al., Biokhimiya, 45, 644-651 (1980), the disclosure of which is incorporated herein by reference. During the fifth step (DEAE column at pH 7.5), an assay is made for contaminating deoxyribonucleases (endonucleases and exonucleases) and only those fractions with polymerase activity and minimal nuclease contamination are pooled. The last chromatographic purification step uses a phosphocellulose column suggested by Chien et al., J. Bacteriol., 127: 1550-1557 (1976), the disclosure of which is incorporated herein by reference. Nuclease(s) and polymerase activities are assayed, and only those polymerase fractions with minimal nuclease contamination are pooled.
While Kaledin et al. and Chien et al. report a purified enzyme with a molecular weight of 62-63 kdaltons, data using the purified protocol described above suggest a molecular weight of about 86-90 kdaltons.
In general, the amplification process involves a chain reaction for producing, in exponential quantities relative to the number of reaction steps involved, at least one specific nucleic acid sequence given (a) that the ends of the required sequence are known in sufficient detail that oligonucleotides can be synthesized which will hybridize to them, and (b) that a small amount of the sequence is available to initiate the chain reaction. The product of the chain reaction will be a discrete nucleic acid duplex with termini corresponding to the ends of the specific primers employed.
Any nucleic acid sequence, in purified or nonpurified form, can be utilized as the starting nucleic acid(s), provided it contains or is suspected to contain the specific nucleic acid sequence desired. Thus, the process may employ, for example, DNA or RNA, including messenger RNA, which DNA or RNA may be single-stranded or double-stranded. In addition, a DNA-RNA hybrid which contains one strand of each may be utilized. A mixture of any of these nucleic acids may also be employed, or the nucleic acids produced from a previous amplification reaction herein using the same or different primers may be so utilized. The specific nucleic acid sequence to be amplified may be only a fraction of a larger molecule or can be present initially as a discrete molecule, so that the specific sequence constitutes the entire nucleic acid.
It is not necessary that the sequence to be amplified be present initially in a pure form; it may be a minor fraction of a complex mixture, such as a portion of the B-globin gene contained in whole human DNA (as exemplified in the Saiki et al. article, supra) or a portion of a nucleic acid sequence due to a particular microorganism which organism might constitute only a very minor fraction of a particular biological sample. The starting nucleic acid sequence may contain more than one desired specific nucleic acid sequence which may be the same or different. Therefore, the amplification process is useful not only for producing large amounts of one specific nucleic acid sequence, but also for amplifying simultaneously more than one different specific nucleic acid sequence located on the same or different nucleic acid molecules.
The nucleic acid(s) may be obtained from any source, for example, from plasmids such as pBR322, from cloned DNA or RNA, or from natural DNA or RNA from any source, including bacteria, yeast, viruses, organelles, and higher organisms such as plants or animals. DNA or RNA may be extracted from blood, tissue material such as chorionic villi, or amniotic cells by a variety of techniques such as that described by Maniatis et al., Molecular Cloning (1982), 280-231.
If probes are used which are specific to a sequence being amplified and thereafter detected, the cells may be directly used without extraction of the nucleic acid if they are suspended in hypotonic buffer and heated to about 90.degree.-100.degree. C., until cell lysis and dispersion of intracellular components occur, generally 1 to 15 minutes. After the heating step the amplification reagents may be added directly to the lysed cells.
Any specific nucleic acid sequence can be produced by the amplification process. It is only necessary that a sufficient number of bases at both ends of the sequence be known in sufficient detail so that two oligonucleotide primers can be prepared which will hybridize to different strands of the desired sequence and at relative positions along the sequence such that an extension product synthesized from one primer, when it is separated from its template (complement), can serve as a template for extension of the other primer into a nucleic acid sequence of defined length. The greater the knowledge about the bases at both ends of the sequence, the greater can be the specificity of the primers for the target nucleic acid sequence, and thus the greater the efficiency of the process.
It will be understood that the world "primer" as used hereinafter may refer to more than one primer, particularly in the case where there is some ambiguity in the information regarding the terminal sequence(s) of the fragment to be amplified. For instance, in the case where a nucleic acid sequence is inferred from protein sequence information, a collection of primers containing sequences representing all possible codon variations based on degeneracy of the genetic code will be used for each strand. One primer from this collection will be homologous with the end of the desired sequence to be amplified.
The oligonucleotide primers may be prepared using any suitable method, such as, for example, the phosphotriester and phosphodiester methods described above, or automated embodiments thereof. In one such automated embodiment, diethylphosphoramidites are used as starting materials and may be synthesized as described by Beaucage et al., Tetrahedron Letters (1981), 22: 1859-1862. One method for synthesizing oligonucleotides on a modified solid support is described in U.S. Pat. No. 4,458,066. It is also possible to use a primer which has been isolated from a biological source (such as a restriction endonuclease digest).
The specific nucleic acid sequence is produced by using the nucleic acid containing that sequence as a template. The first step involves contacting each nucleic acid strand with four different nucleotide triphosphates and one oligonucleotide primer for each different nucleic acid sequence being amplified or detected. If the nucleic acids to be amplified or detected are DNA, then the nucleotide triphosphates are dATP, dCTP, dGTP and TTP.
The nucleic acid strands are used as a template for the synthesis of additional nucleic acid strands. This synthesis can be performed using any suitable method. Generally it occurs in a buffered aqueous solution, preferably at a ph of 7-9, most preferably about 8. Preferably, a molar excess (for cloned nucleic acid, usually about 1000:1 primer:template, and for genomic nucleic acid, usually about 10.sup.6 :1 primer:template) of the two oligonucleotide primers is added to the buffer containing the separated template strands. It is understood, however, that the amount of complementary strand may not be known if the process herein is used for diagnostic applications, so that the amount of primer relative to the amount of complementary strand cannot be determined with certainty. As a practical matter, however, the amount of primer added will generally be in molar excess over the amount of complementary strand (template) when the sequence to be amplified is contained in a mixture of complicated long-chain nucleic acid strands. A large molar excess is preferred to improve the efficiency of the process.
The resulting solution is then treated according to whether the nucleic acids being amplified or detected are double or single-stranded. If the nucleic acids are single-stranded, then no denaturation step need be employed, and the reaction mixture is held at a temperature which promotes hybridization of the primer to its complementary target (template) sequence. Such temperature is generally from about 35.degree. to about 65.degree. C. or more, preferably about 37.degree. C. to about 50.degree. C., for an effective time, generally one-half to five minutes, preferably one-three minutes.
The complement to the original single-stranded nucleic acid may be synthesized by adding one or two oligonucleotide primers thereto. If an appropriate single primer is added, a primer extension product is synthesized in the presence of the primer, the thermostable enzyme and the nucleotide triphosphates. The product will be partially complementary to the single-stranded nucleic acid and will hybridize with the nucleic acid strand to form a duplex of strands of unequal length which may then be separated into single strands as described above to produce two single separated complementary strands. Alternatively, two appropriate primers may be added to the single-stranded nucleic acid and the reaction carried out.
If the nucleic acid contains two strands, it is necessary to separate the strands of the nucleic acid before it can be used as the template. This strand separation can be accomplished by any suitable denaturing method including physical, chemical or enzymatic means. One preferred physical method of separating the strands of the nucleic acid involves heating the nucleic acid until it is completely (>99%) denatured. Typical heat denaturation involves temperatures ranging from about 90.degree. to 105.degree. C. for times generally ranging from about 0.5 to 5 minutes. Preferably the effective denaturing temperature is 90.degree.-100.degree. C. for 0.5 to 3 minutes. Strand separation may also be induced by an enzyme from the class of enzymes known as helicases or the enzyme RecA, which has helicase activity and in the presence of riboATP is known to denature DNA. The reaction conditions suitable for separating the strands of nucleic acids with helicases are described by Kuhn Hoffmann-Barling, CSH-Quantitative Biology, 43: 63 (1978), and techniques for using RecA are reviewed in C. Radding, Ann. Rev. Genetics, 16: 405-37 (1982). The denaturation produces two separated complementary strands of equal or unequal length.
If the double-stranded nucleic acid is denatured by heat, the reaction mixture is allowed to cool to a temperature which promotes hybridization of each primer present to its complementary target (template) sequence. This temperature is usually from about 35.degree. to 65.degree. C. or more, preferably from about 37.degree. C. to about 50.degree. C., maintained for an effective time, generally 0.5 to 5 minutes, and preferably 1-3 minutes. In practical terms, the temperature is simply lowered from about 95.degree. C. to about 65.degree. C. or to as low as 37.degree. C. and hybridization occurs at a temperature within this range.
Whether the nucleic acid is single- or double-stranded, the thermostable enzyme may be added at the denaturation step or when the temperature is being reduced to or is in the range for promoting hybridization. The reaction mixture is then heated to a temperature at which the activity of the enzyme is promoted or optimized, i.e., a temperature sufficient to increase the activity of the enzyme in facilitating synthesis of the primer extension products from the hybridized primer and template. The temperature must actually be sufficient to synthesize an extension product of each primer which is complementary to each nucleic acid template, but must not be so high as to denature each extension product from its complementary template (i.e., the temperature is generally less than about 80.degree.-90.degree. C.).
Depending mainly on the types of enzyme and nucleic acid(s) employed, the typical temperature effective for this synthesis reaction generally ranges from about 40.degree. to 80.degree. C., preferably 50.degree.-70.degree. C. The temperature more preferably ranges from about 60.degree.-65.degree. C. when a polymerase from Thermus aquaticus is employed. The period of time required for this synthesis may range from about 0.5 to 40 minutes or more, depending mainly on the temperature, the length of the nucleic acid, the enzyme and the complexity of the nucleic acid mixture, preferably 1 to 3 minutes. If the nucleic acid is longer, a longer time period is generally required. Preferably, an amount of dimethylsulfoxide (DMSO) which is sufficient to facilitate detection of amplified product is also present in the reaction mixture. The DMSO may be added at any step of the process herein, but preferably is present at this step and at all succeeding steps. Most preferably, 5-10% by volume of DMSO is present.
The newly synthesized strand and its complementary nucleic acid strand form a double-stranded molecule which is used in the succeeding steps of the process. In the next step, the strands of the double-stranded molecule are separated by heat denaturation at a temperature effective to denature the molecule, but not so high that the thermostable enzyme is completely and irreversibly denatured or inactivated. Depending mainly on the type of enzyme and the length of nucleic acid, this temperature generally ranges from about 90.degree. to 105.degree. C., more preferably 90.degree.-100.degree. C., and the time for denaturation typically ranges from 0.5 to four minutes, depending mainly on the temperature and the nucleic acid length.
After this time, the temperature is decreased to a level which promotes hybridization of the primer to its complementary single-stranded molecule (template) produced from the previous step. Such temperature is described above.
After this hybridization step, or in lieu of (or concurrently with) the hybridization step, the temperature is adjusted to a temperature which is effective to promote the activity of the thermostable enzyme to enable synthesis of a primer extension product using as template the newly synthesized strand from the previous step. The temperature again must not be so high as to separate (denature) the extension product from its template, as previously described (usually from 40.degree. to 80.degree. C. for 0.5 to 40 minutes, preferably 50.degree. to 70.degree. C. for 1-3 minutes). Hybridization may occur during this step, so that the previous step of cooling after denaturation is not required. In such a case using simultaneous steps, a temperature range of 50.degree.-70.degree. C. is preferred.
The heating and cooling steps of strand separation, hybridization, and extension product synthesis can be repeated as often as needed to produce the desired quantity of the specific nucleic acid sequence, depending on the ultimate use. The only limitation is the amount of the primers, the thermostable enzyme and the nucleotide triphosphates present. Preferably, the steps are repeated at least once. For use in detection, the number of cycles will depend, e.g., on the nature of the sample. For example, fewer cycles will be required if the sample being amplified is pure. If the sample is a complex mixture of nucleic acids, more cycles will be required to amplify the signal sufficiently for its detection. For general amplification and detection, preferably the process is repeated at least 20 times.
When labeled sequence-specific probes are employed as described below, preferably the steps are repeated at least five times. When human genomic DNA is employed with such probes, the process is repeated preferably 15-30 times to amplify the sequence sufficiently that a clearly detectable signal is produced, i.e., so that background noise does not interfere with detection.
As will be described in further detail below, the amount of the specific nucleic acid sequence produced will accumulate in an exponential fashion.
No additional nucleotides, primers, or thermostable enzyme need be added after the initial addition, provided that the enzyme has not become denatured or inactivated irreversibly, in which case it is necessary to replenish the enzyme after each denaturing step. Addition of such materials at each step, however, will not adversely affect the reaction.
When it is desired to produce more than one specific nucleic acid sequence from the first nucleic acid or mixture of nucleic acids, the appropriate number of different oligonucleotide primers are utilized. For example, if two different specific nucleic acid sequences are to be produced, four primers are utilized. Two of the primers are specific for one of the specific nucleic acid sequences and the other two primers are specific for the second specific nucleic acid sequence. In this manner, each of the two different specific sequences can be produced exponentially by the present process.
For embodiments with a liquid handling capability, the PCR method can be performed in a step-wise fashion where after each step new reagents are added, or simultaneously, where all reagents are added at the initial step, or partially step-wise and partially simultaneous, where fresh reagent is added after a given number of steps. If a method of strand separation, such as heat, is employed which will inactivate the inducing agent, as in the case of a heat-labile enzyme, then it is necessary to replenish the inducing agent after every strand separation step. The simultaneous method may be utilized when an enzymatic means is used for the strand separation step. In the simultaneous procedure, the reaction mixture may contain, in addition to the nucleic acid strand(s) containing the desired sequence, the strand-separating enzyme (e.g., helicase), an appropriate energy source for the strand-separating enzyme, such as rATP, the four nucleotides, the oligonucleotide primers in molar excess, and the inducing agent, e.g., Klenow fragment of E. coli DNA polymerase I. If heat is used for denaturation in a simultaneous process, a heat-stable inducing agent such as a thermostable polymerase may be employed which will operate at an elevated temperature, preferably 65.degree.-90.degree. C. depending on the inducing agent, at which temperature the nucleic acid will consist of single and double strands in equilibrium. For smaller lengths of a nucleic acid sequence, lower temperatures of about 50.degree. C. may be employed. The upper temperature will depend on the temperature at which the enzyme will degrade or the temperature above which an insufficient level of primer hybridization will occur. Such a heat-stable enzyme is described, e.g., by A. S. Kaledin et al., Biokhimiya, 45, 644-651 (1980). Each step of the process will occur sequentially notwithstanding the initial presence of all the reagents. Additional materials may be added as necessary.
The PCR process may be conducted continuously. In one embodiment of the automated process, the reaction may be cycled through a denaturing region, a reagent addition region, and a reaction region. In another embodiment, the enzyme used for the synthesis of primer extension products can be immobilized in a column. The other reaction components can be continuously circulated by a pump through the column and a heating coil in series, thus the nucleic acids produced can be repeatedly denatured without inactivating the enzyme.
After the appropriate length of time has passed to produce he desired amount of the specific nucleic acid sequence, the reaction may be halted by inactivating the enzyme in any known manner or by separating the components of the reaction.
The present invention is demonstrated diagrammatically below, where double-stranded DNA containing the desired sequence [S] comprised of complementary strands [S.sup.+ ] and [S.sup.- ] is utilized as the nucleic-acid. During the first and each subsequent reaction cycle, extension of each oligonucleotide primer on the original template will produce one new ssDNA molecule product of indefinite length which terminates with only one of the primers. These products, hereafter referred to as "long products," will accumulate in a linear fashion; that is, the amount present after any number of cycles will be proportional to the number of cycles.
The long products thus produced will act as templates for one or the other of the oligonucleotide primers during subsequent cycles and will produce molecules of the desired sequence [S.sup.+ ] or [S.sup.- These molecules will also function as templates for one or the other 5 of the oligonucleotide primers, producing further [S.sup.+ ] and [S.sup.- ], and thus a chain reaction can be sustained which will result in the accumulation of [S] at an exponential rate relative to the number of cycles.
By-products formed by oligonucleotide hybridizations other than those intended are not self-catalytic (except in rare instances) and thus accumulate at a linear rate.
The specific sequence to be amplified, [S], can be depicted diagrammatically as: ##STR1## The appropriate oligonucleotide primers would be: ##STR2## so that if DNA containing [S] . . . zzzzzzzzzzzzzzzzAAAAAAAAAAXXXXXXXXXXCCCCCCCCCCzzzzzzzzzzzzzzzz . . .
. . zzzzzzzzzzzzzzzzTTTTTTTTTTYYYYYYYYYYGGGGGGGGGGzzzzzzzzzzzzzzzz . . .
is separated into single strands and its single strands are hybridized to Primers 1 and 2, the following extension reactions can be catalyzed by a thermostable polymerase in the presence of the four nucleotide triphosphates: ##STR3## If these four strands are allowed to rehybridize with Primers 1 and 2 in the next cycle, the thermostable polymerase will catalyze the following reactions: ##STR4## If the strands of the above four duplexes are separated, the following strands are found: ##STR5##
It is seen that each strand which terminates with the oligonucleotide sequence of one primer and the complementary sequence of the other is the specific nucleic acid sequence [S] that is desired to be produced.
The amount of original nucleic acid remains constant in the entire process, because it is not replicated. The amount of the long products increases linearly because they are produced only from the original nucleic acid. The amount of the specific sequence increases exponentially. Thus, the specific sequence will become the predominant species. This is illustrated in the following table, which indicates the relative amounts of the species theoretically present after n cycles, assuming 100% efficiency at each cycle:
When a single-stranded nucleic acid is utilized as the template, only one long product is formed per cycle.
A sequence within a given sequence can be amplified after a given number of amplifications to obtain greater specificity of the reaction by adding after at least one cycle of amplification a set of primers which are complementary to internal sequences (which are not on the ends) of the sequence to be amplified. Such primers may be added at any stage and will provide a shorter amplified fragment. Alternatively, a longer fragment can be prepared by using primers with non-complementary ends but having some overlap with the primers previously utilized in the amplification.
The amplification method may be utilized to clone a particular nucleic acid sequence for insertion into a suitable expression vector. The vector may be used to transform an appropriate host organism to produce the gene product of the sequence by standard methods of recombinant DNA technology. Such cloning may involve direct ligation into a vector using blunt-end ligation, or use of restriction enzymes to cleave at sites contained within the primers.
In addition, the amplification process can be used for in vitro mutagenesis. The oligodeoxyribonucleotide primers need not be exactly complementary to the DNA sequence which is being amplified. It is only necessary that they be able to hybridize to the sequence sufficiently well to extended by the thermostable enzyme. The product of an amplification reaction wherein the primers employed are not exactly complementary to the original template will contain the sequence of the primer rather than the template, thereby introducing an in vitro mutation. In further cycles this mutation will be amplified with an undiminished efficiency because no further mispaired priming are required. The mutant thus produced may be inserted into an appropriate vector by standard molecular biological techniques and might confer mutant properties on this vector such as the potential for production of an altered protein.
The process of making an altered DNA sequence as described above could be repeated on the altered DNA using different primers to induce further sequence changes. In this way, a series of mutated sequences could gradually be produced wherein each new addition to the series could differ from the last in a minor way, but from the original DNA source sequence in an increasingly major way. In this manner, changes could be made ultimately which were not feasible in a single step due to the inability of a very seriously mismatched primer to function.
In addition, the primer can contain as part of its sequence a non-complementary sequence, provided that a sufficient amount of the primer contains a sequence which is complementary to the strand to be amplified. For example, a nucleotide sequence which is not complementary to the template sequence (such as, e.g., a promoter, linker, coding sequence, etc.) may be attached at the 5' end of one or both of the primers, and thereby appended to the product of the amplification process. After the extension primer is added, sufficient cycles are run to achieve the desired amount of new template containing the non-complementary nucleotide insert. This allows production of large quantities of the combined fragments in a relatively short period of time (e.g., two hours or less) using a simple technique.
The amplification method may also be used to enable detection and/or characterization of specific nucleic acid sequences associated with infectious diseases, genetic disorders or cellular disorders such as cancer, e.g., oncogenes. Amplification is useful when the amount of nucleic acid available for analysis is very small, as, for example, in the prenatal diagnosis of sickle cell anemia using DNA obtained from fetal cells. Amplification is particularly useful if such an analysis is to be done on a small sample using nonradioactive detection techniques which may be inherently insensitive, or where radioactive techniques are being employed, but where rapid detection is desirable.
For the purposes of this discussion, genetic diseases may include specific deletions and/or mutations in genomic DNA from any organism, such as, e.g., sickle cell anemia, a-thalassemia, B-thalassemia, and the like. Sickle cell anemia can be readily detected via oligomer restriction analysis as described by EP Patent Publication 164,054 published Dec. 11, 1985, or via a RFLP-like analysis following amplification of the appropriate DNA sequence by the amplification method. a-Thalassemia can be detected by the absence of a sequence, and B-thalassemia can be detected by the presence of a polymorphic restriction site closely linked to a mutation that causes the disease.
All of these genetic diseases may be detected by amplifying the appropriate sequence and analyzing it by Southern blots without using radioactive probes. In such a process, for example, a small sample of DNA from, e.g., amniotic fluid containing a very low level of the desired sequence is amplified, cut with a restriction enzyme, and analyzed via a Southern blotting technique. The use of non-radioactive probes is facilitated by the high level of the amplified signal.
In another embodiment, a small sample of DNA may be amplified to a convenient level and then a further cycle of extension reactions performed wherein nucleotide derivatives which are readily detectable (such as .sup.32 p-labeled or biotin-labeled nucleotide triphosphates) are incorporated directly into the final DNA product, which may be analyzed by restriction and electrophoretic separation or any other appropriate method.
In a further embodiment, the nucleic acid may be exposed to a particular restriction endonuclease prior to amplification. Since a sequence which has been cut cannot be amplified, the appearance of an amplified fragment, despite prior restriction of the DNA sample, implies the absence of a site for the endonuclease within the amplified sequence. The presence or absence of an amplified sequence can be detected by an appropriate method.
A practical application of the amplification technique, that is, in facilitating the detection of sickle cell anemia via the oligomer restriction technique [described in EP 164,054, supra, and by Saiki et al., Bio/Technology, Vol. 3, pp. 1008-1012 (1985)] is described in detail in the Saiki et al. Science article cited above. In that Science article, a specific amplification protocol is exemplified using a B-globin gene segment.
The amplification method herein may also be used to detect directly single-nucleotide variations in nucleic acid sequence (such as genomic DNA) using sequence-specific oligonucleotides, as described more fully in U.S. Ser. No. 839,331, filed Mar. 13, 1986, now abandoned and in U.S. Ser. No. 899,344, filed Aug. 22, 1986, now abandoned (Cetus Case 2262.1), which is a continuation-in-part of U.S. Ser. No. 839,331, the disclosures of both of which are incorporated herein by reference.
Briefly, in this process, the amplified sample is spotted directly on a series of membranes, and each membrane is hybridized with a different labeled sequence-specific oligonucleotide probe. After hybridization the sample is washed and the label is detected. This technique is especially useful in detecting DNA polymorphisms.
Various infectious diseases can be diagnosed by the presence in clinical samples of specific DNA sequences characteristic of the causative microorganism. These include bacteria, such as Salmonella, Chlamydia, Neisseria; viruses, such as the hepatitis viruses, and parasites, such as the Plasmodium responsible for malaria. U.S. Patent Reexamination Certificate B1 4,358,535 issued to Falkow et al. on May 13, 1986 describes the use of specific DNA hybridization probes for the diagnosis of infectious diseases. A relatively small number of pathogenic organisms may be present in a clinical sample from an infected patient and the DNA extracted from these may constitute only a very small fraction of the total DNA tn the sample. Specific amplification of suspected sequences prior to immobilization and detection by hybridization of the DNA samples could greatly improve the sensitivity and specificity of traditional procedures.
Routine clinical use of DNA probes for the diagnosis of infectious diseases would be simplified considerably if non-radioactively labeled probes could be employed as described in EP 63,879 to Ward. In this procedure biotin-containing DNA probes are detected by chromogenic enzymes linked to avidin or biotin-specific antibodies. This type of detection is convenient, but relatively insensitive. The combination of specific DNA amplification by the present method and the use of stably labeled probes could provide the convenience and sensitivity required to make the Falkow et al. and Ward procedures useful in a routine clinical setting.
A specific use of the amplification technology for detecting or monitoring for the AIDS virus is described in U.S. application Ser. No. 818,127, filed Jan. 10, 1986, now abandoned, the disclosure of which is incorporated herein by reference. Briefly, the amplification and detection process is used with primers and probes which are designed to amplify and detect, respectively, nucleic acid sequences which are substantially conserved among the nucleic acids in AIDS viruses and specific to the nucleic acids in AIDS viruses. Thus, the sequence to be detected must be sufficiently complementary to the nucleic acids in AIDS viruses to initiate polymerization preferably at room temperature in the presence of the enzyme and nucleotide triphosphates.
The amplification process can also be utilized to produce sufficient quantities of DNA from a single copy human gene such that detection by a simple non-specific DNA stain such as ethidium bromide cna be employed to diagnose DNA directly.
In addition to detecting infectious diseases and pathological abnormalities in the genome of organisms, the amplification process can also be used to detect DNA polymorphisms which may not be associated with any pathological state.
In summary, the amplification process is seen to provide a process for amplifying one or more specific nucleic acid sequences using a chain reaction and a thermostable enzyme, in which reaction primer extension products are produced which can subsequently act as templates for further primer extension reactions. The process is especially useful in detecting nucleic acid sequences which are initially present in only very small amounts.
The following examples are offered by way of illustration only and are by no means intended to limit the scope of the claimed invention. In these samples, all percentages are by weight if for solid and by volume if for liquids, and all temperatures are given in degrees Celsius.
Example I
I. Synthesis of the Primers
The following two oligonucleotide primers were prepared by the method described below:
These primers, both 20-mers, anneal to opposite strands of the genomic DNA with their 5' ends separated by a distance of 110 base pairs.
A. Automated Synthesis Procedures: The diethylphosphoramidites,: synthesized according to Beaucage and Caruthers (Tetrahedron Letters (1981) 22: 1859-1862) were sequentially condensed to a nucleoside derivatized controlled pore glass support using a Biosearch SAM-1. The procedure included detritylation with trichloroacetic acid in dichloromethane, condensation using benzotriazole as activating proton donor, and capping with acetic anhydride and dimethylaminopyridine in tetrahydrofuran and pyridine. Cycle time was approximately 30 minutes. Yields at each step were essentially quantitative and were determined by collection and spectroscopic examination of the dimethoxytrityl alcohol released during detritylation.
B. Oligodeoxyribonucleotide Deprotection and Purification Procedures: The solid support was removed from the column and exposed to 1 ml concentrated ammonium hydroxide at room temperature for four hours in a closed tube. The support was then removed by filtration and the solution containing the partially protected oligodeoxynucleotide was brought to 55.degree. C. for five hours. Ammonia was removed and the residue was applied to a preparative polyacrylamide gel. Electrophoresis was carried out at 30 volts/cm for 90 minutes after which the band containing the product was identified by UV shadowing of a fluorescent plate. The band was excised and eluted with 1 ml distilled water overnight at 4.degree. C. This solution was applied to an Altech RP18 column and eluted with a 7-13% gradient of acetonitrile in 1% ammonium acetate buffer at pH 6.0. The elution was monitored by UV5 absorbance at 260 nm and the appropriate fraction collected, quantitated by UV absorbance in a fixed volume and evaporated to dryness at room temperature in a vacuum centrifuge.
C. Characterization of Oligodeoxyribonucleotides: Test aliquots of the purified oligonucleotides were 32p labeled with polynucleotide kinase and y-32p-ATP. The labeled compounds were examined by autoradiography of 14-20% polyacrylamide gels after electrophoresis for 45 minutes at 50 volts/cm. This procedure verifies the molecular weight. Base composition was determined by digestion of the oligodeoxyribonucleotide to nucleosides by use of venom diesterase and bacterial alkaline phosphatase and subsequent separation and quantitation of the derived nucleosides using a reverse phase HPLC column and a 10% acetonitrile, 1% ammonium acetate mobile phase.
II. Isolation of Human Genomic DNA from Cell Line
High molecular weight genomic DNA was isolated from a T cell line, Molt 4, homozygous for normal B-globin available from the Human Genetic Mutant Cell Depository, Camden, N.J. as GM2219C using essentially the method of Maniatis et al., Molecular Cloning (1982), 280-281.
III. Purification of a Polymerase From Thermus aquaticus
Thermus aquaticus strain YT1, available without restriction from the American Type Culture Collection, 12301 Parklawn Drive, Rockville, Md., as ATCC No. 25,104 was grown in flasks in the following medium:
A 10-liter fermentor was inoculated from a seed flask cultured overnight in the above medium at 70.degree. C. A total of 600 ml from the seed flask was used to inoculate 10 liters of the same medium. The pH was controlled at 8.0 with ammonium hydroxide with the dissolved oxygen at 40%, with the temperature at 70.degree. C., and with the stirring rate at 400 rpm.
After growth of the cells, they were purified using the protocol (with slight modification) of Kaledin et al., supra, through the first five stages and using a different protocol for the sixth stage. All six steps were conducted at 4.degree. C. The rate of fractionation on columns was 0.5 column volumes/hour and the volumes of gradients during elution were 10 column volumes.
Briefly, the above culture of the T. aquaticus cells was harvested by centrifugation after nine hours of cultivation, in late log phase, at a cell density of 1.4 9 dry weight/l. Twnety grams of cells was resuspended in 80 ml of a buffer consisting of 50 mM Tris-HCl pH 7.5, 0.1 mM EDTA. Cells were lysed and the lysate was centrifuged for two hours at 35,000 rpm in a Beckman TI 45 rotor at 4.degree. C. The supernatant was collected (fraction A) and the protein fraction precipitating between 45 and 75.times. saturation of ammonium sulfate was collected, dissolved in a buffer consisting of 0.2M potassium phosphate buffer, pH 6.5, 10 mM 2-mercaptoethanol, and 5% glycerine, and finally dialyzed against the same buffer to yield fraction B.
Fraction B was applied to a 2.2.times.30-cm column of DEAE-cellulose, equilibrated with the above described buffer. The column was then washed with the same buffer and the fractions containing protein (determined by absorbance at 280 nm) were collected. The combined protein fraction was dialyzed against a second buffer, containing 0.01M potassium phosphate buffer, pH 7.5, 10 mM 2-mercaptoethanol, and 5% glycerine, to yield fraction C.
Fraction C was applied to a 26.times.21-cm column of hydroxyapatite, equilibrated with a second buffer. The column was then washed and the enzyme was eluted with a linear gradient of 0.010.5M potassium phosphate buffer, pH 7.5, containing 10 mM 2-mercaptoethanol and 5% glycerine. Fractions containing DNA polymerase activity (90-180 mM potassium phosphate) were combined, concentrated four-fold using an Amicon stirred cell and YM10 membrane, and dialyzed against the second buffer to yield fraction D.
Fraction D was applied to a 1.6.times.28-cm column of DEAE-cellulose, equilibrated with the second buffer. The column was washed and the polymerase was-eluted with a linear gradient of 0.01-0.5M potassium phosphate in the second buffer. The fractions were assayed for contaminating endonuclease(s) and exonuclease(s) by electrophoretically detecting the change in molecular weight of phage DNA or supercoiled plasma DNA after incubation with an excess of DNA polymerase (for endonuclease) and after treatment with a restriction enzyme that cleaves the DNA into several fragments (for exonuclease). Only those DNA polymerase fractions (65-95 mM potassium phosphate) having minimal nuclease contamination were pooled. To the pool was added autoclaved gelatin in an amount of 250 .mu.g/ml, and dialysis was conducted against the second buffer to yield Fraction E.
Fraction E was applied to a 9 ml phosphocellulose column and eluted with a 100 ml gradient (0.01-0.4M KCl gradient in 20 mM potassium phosphate buffer pH 7.5). The fractions were assayed for contaminating endo/exonuclease(s) as described above as well as for polymerase activity (by the method of Kaledin et al.) and then pooled. The pooled fractions were dialyzed against the second buffer, then concentrated by dialysis against 50% glycerine and the second buffer.
The molecular weight of the polymerase was determined by SDS PAGE. Marker proteins (Bio-Rad low molecular weight standards) were phosphorylase B (92,500), bovine serum albumin (66,200), ovalbumin (45,000), carbonic anhydrase (31,000), soybean trypsin inhibitor (21,500), and lysozyme (14,400).
Preliminary data suggest that the polymerase has a molecular weight of about 86,000-90,000 daltons, not 62,000-63,000 daltons reported in the literature (e.g., by Kaledin et al.).
IV. Amplification Reaction
One microgram of the genomic DNA described above was diluted in an initial 100 .mu.l aqueous reaction volume containing 25 mM Tris.multidot.HCl buffer (pH 8.0), 50 mM KCl, 10 mM MgCl.sub.2, 5 mM dithiothreitol, 200 .mu.g/ml gelatin, 1 .mu.M of primer PC03, 1 .mu.M of primer PC04, 1.5 mM dATP, 1.5 .mu.M dCTP, 1.5 mM dGTP and 1.5 mM TTP. The sample was heated for 10 minutes at 98.degree. C. to denature the genomic DNA, then cooled to room temperature. Four microliter of the polymerase from Thermus aquaticus was added to the reaction mixture and overlaid with a 100 .mu.l mineral oil cap. The sample was then placed in the aluminum heating block of the liquid handling and heating instrument described in U.S. application Ser. No. 833,368 filed Feb. 25, 1986, now abandoned the disclosure of which is incorporated herein by reference.
The DNA sample underwent 20 cycles of amplification in the machine, repeating the following program cycle:
1) heating from 37.degree. C. to 98.degree. C. in heating block over a period of 2.5 minutes; and
2) cooling from 98.degree. C. to 37.degree. C. over a period of three minutes to allow the primers and DNA to anneal.
After the last cycle, the sample was incubated for an additional 10 minutes at 55.degree. C. to complete the final extension reaction.
V. Synthesis and Phosphorylation of Oligodeoxyribonucleotide Probes
A labeled DNA probe, designated RS24, of the following sequence was prepared:
where * indicates the label. This probe is 40 bases long, spans the fourth through seventeenth codons of the gene, and is complementary to the normal .beta.-globin allele (.beta..sup.A). The schematic diagram of primers and probes is given below: ##STR6##
This probe was synthesized according to the procedures described in Section I of Example I. The probe was labeled by contacting 20 pmole thereof with 4 units of T4 polynucleotide kinase (New England Biolabs) and about 40 pmole .sup.-32 P-ATP (New England Nuclear, about 7000 Ci/mmole) in a 40 .mu.l reaction volume containing 70 mM Tris buffer (pH 7.6), 10 mM .mu.gCl.sub.2, 1.5 rM spermine and 10 mM dithiothreitol for 60 minutes at 37.degree. C. The total volume was then adjusted to 100 .mu.l with 25 mM EDTA and purified according to the procedure of Maniatis et al., Molecular Cloning (1982), 466-467 over a 1 ml Bio Gel P-4 (Bio-Rad) spin dialysis column equilibrated with Tris-EDTA (TE) buffer (10 mM Tris buffer, 0.1 mM EDTA, pH 8.0). TCA precipitation of the reaction product indicated that for RS24 the specific activity was 4.3 .mu.Ci/pmole and the final concentration was 0.118 pmole/.mu.l.
VI. Dot Blot Hybridizations
Four microliter of the amplified sample from Section I and 5.6 .mu.l of appropriate dilutions of B-globin plasmid DNA calculated to represent amplification efficiencies of 70, 75, 80, 85, 90, 95 and 100% were diluted with 200 .mu.l 0.4 H NaOH, 25 mM EDTA and spotted onto a Genatran 45 (Plasco) nylon filter by first wetting the filter with water, placing it in a Bio-Dot (Bio-Rad, Richmond, Calif.) apparatus for preparing dot blots which holds the filters in place, applying the samples, and rinsing each well with 0.1 ml of 20.times. SSPE (3.6M NaCl, 200 mM NaH.sub.2 PO.sub.4, 20 mM EDTA), as disclosed by Reed and Mann, Nucleic Acids Research, 13, 7202-7221 (1985). The filters were then removed, rinsed in 20.times. SSPE, and baked for 30 minutes at 80.degree. C. in a vacuum oven.
After baking, each filter was then contacted with 16 ml of a hybridization solution consisting of 3.times. SSPE, 5.times. Denhardt's solution (1.times.=0.02% polyvinylpyrrolidone, 0.02.times. Ficoll, 0.02% bovine serum albumin,, 0.2 mM Tris, 0.2 mM EDTA, pH 8.0), 0.5% SDS, and 30% formamide, and incubated for two hours at 42.degree. C. Then 2 pmole of probe RS24 was added to the hybridization solution and the filter was incubated for two hours at 42.degree. C.
Finally, each hybridized filter was washed twice with 100 ml of 2.times. SSPE and 0.1% SDS for 10 minutes at room temperature. Then the filters were treated once with 100 ml of 2.times. SSPE, 0.1% SDS at 60.degree. C. for 10 minutes.
Each filter was then autoradiographed, with the signal readily apparent after two hours.
VII. Discussion of Autoradiogram
The autoradiogram of the dot blots was analyzed after two hours and compared in intensity to standard serial dilution .beta.-globin reconstructions prepared with HaeIII/MaeI-digested pBR:.beta..sup.A, where .beta..sup.A is the wild-type allele, as described in Saiki et al., Science, supra. Analysis of the reaction product indicated that the overall amplification efficiency was about 95%, corresponding to a 630,000-fold increase in the .beta.-globin target sequence.
Example Ii
I. Amplification Reaction
Two 1 .mu.9 samples of genomic DNA extracted from the Molt 4 cell line as described in Example I were each diluted in a 100 .mu.l reaction volume containing 50 mM KCl, 25 mM Tris HCl buffer pH 8.0, 10 mM MgCl.sub.2, 1 .mu.M of primer PC03, 1 .mu.M of primer PC04, 200 .mu.g/ml gelatin, 10% dimethylsulfoxide (by volume), 1.5 mM dATP, 1.5 mM dCTP, 1.5 mM dGTP, and 1.5 mM TTP. After this mixture was heated for 10 minutes at 98.degree. C. to denature the genomic DNA, the samples were cooled to room temperature and 4 .mu.l of the polymerase from Thermus aquaticus described in Example I was added to each sample. The samples were overlaid with mineral oil to prevent condensation and evaporative loss.
One of the samples was placed in the heating block of the machine described in Example I and subjected to 25 cycles of amplification, repeating the following program cycle:
(1) heating from 37.degree. to 93.degree. C. over a period of 2.5 minutes;
(2) cooling from 93.degree. C. to 37.degree. C. over a period of three minutes to allow the primers and DNA to anneal; and
(3) maintaining at 37.degree. C. for two minutes.
After the last cycle the sample was incubated for an additional 10 minutes at 60.degree. C. to complete the final extension reaction.
The second sample was placed in the heat-conducting container of the machine, described in more detail herein, supra. The heat-conducting container is attached to Peltier heat pumps which adjust the temperature upwards or downwards and a microprocessor controller to control automatically the amplification sequence, the temperature levels, the temperature ramping and the timing of the temperature.
The second sample was subjected to 25 cycles of amplification, repeating the following program cycle:
(1) heating from 37.degree. to 95.degree. C. over a period of three minutes;
(2) maintaining at 95.degree. C. for 0.5 minutes to allow denaturation to occur;
(3) cooling from 95.degree. to 37.degree. C. over a period of one minute: and
(4) maintaining at 37.degree. C. for one minute.
II. Analysis
Two tests were done for analysis, a dot blot and an agarose gel analysis.
For the dot blot analysis, a labeled DNA probe, designated RS18, of the following sequence was prepared.
where * indicates the label. This probe is 19 bases long, spans the fourth through seventeenth codons of the gene, and is complementary to the normal .beta.-globin allele (.beta..sup.A). The schematic diagram of primers and probes is given below: ##STR7##
This probe was synthesized according to the procedures described in Section I of Example I. The probe was labeled by contacting 10 pmole thereof with 4 units of T4 polynucleotide kinase (New England Biolabs) and about 40 pmol .sup.-32 P-ATP (New England Nuclear, about 7000 Ci/mmole) in a 40 .mu.l reaction volume containing 70 mM Tris HCl buffer (pH 7.6), 10 mm MgCl.sub.2, 1.5 mM spermine and 10 mM dithiothreitol for 60 minutes at 37.degree. C. The total volume was then adjusted to 100 .mu.l with 25 mM EDTA and purified according to the procedure of Maniatis et al., Molecular Cloning (1982), 466-467 over a 1 ml Bio Gel P-4 (BioRad) spin dialysis column equilibrated with Tris-EDTA (TE) buffer (10 mM Tris-HCl buffer, 0.1 mM EDTA, pH 8.0). TCA precipitation of the reaction product indicated that for RS18 the specific activity was 4.6 .mu.ci/pmole and the final concentration was 0.114 pmole/.mu.l.
Five microliter of the amplified sample from Section I and of a sample amplified as described above except using the Klenow fragment of E. coli DNA Polymerase I instead of the thermostable enzyme were diluted with 195 .mu.l 0.4N NaOH, 25 mM EDTA and spotted onto two replicate Genatran 45 (Plasco) nylon filters by first wetting the filters with water, placing them in a Bio-Dot (Bio-Rad, Richmond, Calif.) apparatus for preparing dot blots which holds the filters in place, applying the samples, and rinsing each well with 0.4 ml of 20.times. SSPE (3.6M NaCl, 200 mM NaH.sub.2 PO.sub.4, 20 mM EDTA), as disclosed by Reed and Mann, Nucleic Acids Research, 13, 7202-7221 (1985). The filters were then removed, rinsed in 20.times. SSPE, and baked for 30 minutes at 80.degree. C. in a vacuum oven.
After baking, each filter was then contacted with 6 ml of a hybridization solution consisting of 5.times. SSPE, 5.times. Denhardt's solution (1.times.=0.02% polyvinylpyrrolidone, 0.02% Ficoll, 0.02% bovine serum albumin, 0.2 nM Tris, 0.2 mM EDTA, pH 8.0) and 0.5% SDS, and incubated for 60 minutes at 55.degree. C. Then 5 .mu.l of probe RS18 was added to the hybridization solution and the filter was incubated for 60 minutes at 55.degree. C.
Finally, each hybridized filter was washed twice with 100 ml of 2.times. SSPE and 0.1% SDS for 10 minutes at room temperature. Then the filters were treated twice more with 100 ml of 5.times. SSPE, 0.1% SDS at 60.degree. C. for 1) one minute and 2) three minutes, respectively.
Each filter was then autoradiographed, with the signal readily apparent after 90 minutes.
In the agarose gel analysis, 5 .mu.l each amplification reaction was loaded onto 4% NuSieve/0.5% agarose gel in 1.times. TBE buffer (0.089M Tris borate, 0.089M boric acid, and 2 mM EDTA) and electrophoresed for 60 minutes at 100 V. After staining with ethidium bromide, DNA was visualized by UV fluorescence.
The results show that the machines used in Example I and this example herein were equally effective in amplifying the DNA, showing discrete high-intensity 110-base pair bands of similar intensity, corresponding to the desired sequence, as well as a few other discrete bands of much lower intensity. In contrast, the amplification method as described in Example I of U.S. application Ser. No. 839,331 filed Mar. 13, 1986, now abandoned, supra, which involves reagent transfer after each cycle using the Klenow fragment of E. coli Polymerase I, gave a DNA smear resulting from the nonspecific amplification of many unrelated DNA sequences.
It is expected that similar improvements in amplification and detection would be achieved in evaluating HLA-DQ, DR and DP regions.
Example Iii
Amplification and Cloning
For amplification of a 119-base pair fragment on the human .beta.-hemoglobin gone, a total of 1 microgram each of human genomic DNA isolated from the Molt 4 cell line or from the GM2064 cell line (representing a homozygous deletion of the .beta.- and -hemoglobin region and available from the Human Genetic Mutant Cell Depository, Camden, N.J.) as described above was amplified in a 100 .mu.l reaction volume containing 50 mM KCl, 25 mM Tris NCl, pH 8, 10 mM MgCl.sub.2, 200 .mu.g/ml gelatin, S mM beta-mercaptoethanol, 1.5 mM dATP, 1.5 mM dCTP, 1.5 mM dTTP, 1.5 mM dGTP, and 1 .mu.M of each of the following primers:
where lower case letters denote mismatches from wild-type sequence to create restriction enzyme sites. GH18 is a 26-base oligonucleotide complementary to the negative strand and contains an internal PstI site. GH19 is a 23-base oligonucleotide complementary to the plus strand and contains an internal HindIII recognition sequence. These primers were selected by first screening the regions of the gene for homology to the PstI and HindIII restriction sites of bacteriophage M13. The primers were then prepared as described in Example I.
The above reaction mixtures were heated for 10 minutes at 95.degree. C. and then cooled to room temperature. A total of 4 .mu.l of the polymerase described in Example I was added to each reaction mixture, and then each mixture was overlayed with mineral oil. The reaction mixtures were subjected to 30 cycles of amplification with the following program:
2.5 min. ramp, 37.degree. to 98.degree. C.
3 min. ramp, 98.degree. to 37.degree. C.
2 min. soak, 37.degree. C.
After the last cycle, the reaction mixtures were incubated for 20 minutes at 65.degree. C. to complete the final extension. The mineral oil was extracted with chloroform and the mixtures were stored at 20.degree. C.
A total of 10 .mu.l of the amplified product has digested with 0.5 .mu.g M13mp10 cloning vector, which is publicly available from Boehringer-Mannheim in a 50 .mu.l volume containing 50 mM NaCl, 10 mM Tris.multidot.HCl, pH 7.8, 10 mM MgCl2, 20 units PstI and 26 units HindIII for 90 minutes at 37.degree. C. The reaction was stopped by freezing at 20.degree. C. The volume was adjusted to 110 .mu.l with TE buffer and loaded (100 .mu.l) onto a 1 ml BioGel P-4 spin dialysis column. One 0.1 ml fraction was collected and ethanol precipitated.
(At this point it was discovered that there was .beta.-globin amplification product in the GM2064 sample. Subsequent experiments traced the source of contamination to the primers, either GH18 or GH19. Because no other source of primers was available, the experiment was continued with the understanding that some cloned sequences would be derived from the contaminating DNA in the primers.)
The ethanol pellet was resuspended in 15 .mu.l water, then adjusted to 20 .mu.l volume containing 50 mM Tris.multidot.HCl, pH 7.8, 10 mM MgCl.sub.2, 0.5 mM ATP, 10 mM dithiothreitol, and 400 units ligase. This mixture was incubated for three hours at 16.degree. C.
Ten microliters of ligation reaction mixture containing Molt 4 DNA was transformed into E. coli strain JM103 competent cells, which are publicly available from BRL in Bethesda, Md. The procedure followed for preparing the transformed strain is described in Messing, J. (1981) Third Cleveland Symposium on Macromolecules:Recombinant DNA, ed. A. Walton, Elsevier, Amsterdam, 143-153. A total of 651 colorless plaques (and O blue plaques) were obtained. Of these, 119 had a (+)-strand insert (18%) and 19 had a (-)-strand insert (3%). This is an increase of almost 20-fold over the percentage of .beta.-globin positive plaques among the primer-positive plaques from the amplification technique using Klenow fragment of E. coli Polymerase I, where the reaction proceeded for two minutes at 25.degree. C., after which the steps of heating to 100.degree. C. for two minutes, cooling, adding Klenow fragment, and reacting were repeated nine times. These results confirm the improved specificity of the amplification reaction employing the thermostable enzyme herein.
In a later cloning experiment with GM2064 and the contaminated primers, 43 out of 510 colorless plaques (8%) had the (+)-strand insert. This suggests that approximately one-half of the 119 clones from volt 4 contain the contaminant sequence.
Ten of the (+)-strand clones from Molt 4 were sequenced. Five were normal wild-type sequence and five had a single C to T mutation in the third position of the second codon of the gene (CAC to CAT). Four of the contaminant clones from GM2064 were sequenced and all four were normal.
Restriction site-modified primers may also be used to amplify and clone and partially sequence the human N-ras oncogene and to clone base pair segments of the HLA DQ-.alpha., DQ-.beta. and DR-.beta. genes using the above technique. All of these amplification reactions may be carried out in the presence of 10% by volume dimethylsulfoxide.
Plating and Screening
The filters were probed with the primer PC04 to determine the percentage of inserts resulting from amplification and cloning. The percentage of B-globin positive plaques among the amplified primer-positive plaques was approximately 20%. This is an increase of 20-fold over the percentage of B-globin positive plaques among the primer-positive plaques from the amplification technique using Klenow fragment of E. coli Polymerase I, where the reaction proceeded for two minutes at 25.degree. C., after which the steps of heating to 100.degree. C. for two minutes, cooling, adding Klenow fragment, and reacting were repeated nine times. These results confirm the improved specificity of the amplification reaction of the invention herein employing a thermostable enzyme.
Restriction site-modified primers may also be used to amplify and clone and partially sequence the human N-ras oncogene and to clone base pair segments of the HLA DQ-.alpha., DQ-.beta., and DR-.beta. genes using the above technique. All of these amplification reactions may be carried out in the presence of 10% by volume dimethylsulfoxide.
In summary, the present invention provides an apparatus for performing automated amplification of one or more nucleic acid sequences involving a temperature-cycled chain reaction and a thermostable enzyme, which apparatus has a heat-conducting container for the reagents, means for heating, cooling and maintaining the container to or at any given temperature, and a computer means to generate signals that control the temperature levels. The amplification process results in increased yields of amplified product, greater specificity, and fewer steps necessary to carry out the procedure over what has been previously disclosed.
Example Iv
Comparative Example of PCR Protocol Run Manually and on Automated PCR Machine
The following example illustrates that equivalent results are obtained when the PCR protocol is run on a machine of the instant invention and when run manually. The results are indicated by the intensity of the dot-blots on an autoradiograph of samples of DNA which had been amplified either manually or on the PCR machine and then hybridized to radioactive probes. These examples are illustrative only and are by no means intended to limit the scope of the claimed invention.
Isolation of Human Genomic DNA from Cell Lines
High molecular weight genomic DNA was isolated from the lymphoid cell lines, Molt4, SC-1 and GM2064 using essentially the method of Maniatis et al., Molecular Cloning (1982), 280-281.
Molt4 (Human Mutant Cell Repository, GM2219C) is a T cell line homozygous for normal .beta.-globin, and SC-1, is an EBV-transformed B cell line homozygous for the sickle cell allele. The cell line SC-1 (CTCC #0082) was deposited on Mar. 19, 1985 with the American Type Culture Collection (ATCC), 12301 Parklawn Drive, Rockville, Md. 20852 USA, with ATCC Accession No. CRL #8756. GM2064 (Human Mutant Cell Repository, GM2064) was originally isolated from an individual homozygous for hereditary persistence of fetal hemoglobin (HPFH) and contains no beta- or delta-globin gene sequences. All cell lines were maintained in RPMI-1640 with 10% fetal calf serum.
Polymerase Chain Reaction to Amplify Selectively DNA Sequences--Automated Samples
Six samples of the above genomic DNA, three from GM2064, two from Molt4 and one from SC-1 were amplified by the automated PCR machine of the instant invention.
In each instance, one microgram of the genomic DNA was amplified in an initial 100 .mu.l reaction volume containing 10 .mu.l of Klenow salts [10 mM Tris buffer (pH 7.5), 50 mM NaCl, 10 mM MgCl.sub.2 ], 10 .mu.l DMSO, 35 .mu.l water, 15 .mu.l of 40 mM deoxynucleotide triphosphate [(dNTP) 10 mM of dATP, dCTP, dGTP and dTTP were used], 10 .mu.l of 10 .mu.M of the primer PC03 [5' ACACAACTGTGTTCACTAGC 3'; Saiki et al., Science, Vol. 230, pp. 1350-54, (Dec. 20, 1985)] and 10 .mu.l of 10 .mu.M of the primer PC04 [3' CCACTTGCACCTACTTCAAC 5'; Saiki et al., id.]. The mixture in an Eppendorf tube for each sample was overlaid with approximately 100 .mu.l of mineral oil to prevent evaporation. The Eppendorf tubes with the samples to be amplified were placed in the heating block (plate 1).
An enzyme mixture was also prepared in Eppendorf tubes placed in the block (plate 2) behind the DNA sample. A 570 .mu.l enzyme preparation was prepared composed of 38 .mu.l of Klenow fragment of E. coli DNA polymerase I (Pharmacia, 5 units per .mu.l which was diluted herein to 0.33 units per .mu.l), 57 .mu.l of Klenow salts and 475 .mu.l of water. The 570 .mu.l enzyme preparation was then divided into six Eppendorf tubes (95 .mu.l each). The tubes were placed in plate 2 which is maintained at a constant temperature of -1.degree. Centigrade. At that temperature of the plate, the enzyme mixture is kept at approximately 2.degree. C. depending on the ambient temperature as stated above.
Each DNA sample underwent 20 cycles of amplification in the PCR machine. The DNA samples were first denatured at approximately 94.degree. to 95.degree. wherein the plate 1 temperature is maintained at 98.degree. C. for eight minutes and then the following cycle was repeated for twenty times:
1) denatured in the PCR heating block (plate 1) for 2.5 minutes;
2) the mixture was then cooled to 37.degree. C., the cooling period being for about three minutes, allowing the primers and genomic DNA to anneal;
3) 3 .mu.l of the enzyme preparation was then transferred automatically by pipette from the back block (plate 2) to the DNA samples held in the heating block (plate 1); by automatic aspiration and redispensing, the enzyme and DNA preparations were mixed;
4) the extension reaction was then allowed to proceed for two minutes at 37.degree. C.
The pipetting speed was rapid. The enzyme tip height was set at 1800 whereas the dispensing height was set at 1740. When plate 1 is cooled to 37.degree. C., the reaction mixture also attains approximately 37.degree. C.
The 20 cycles took approximately 21/2 hours to perform. The samples were not denatured after the last cycle as double-stranded DNA was desired. The oil from each tube was removed with 0.1 .mu.l of chloroform. The final sample volumes in each tube were approximately 160 .mu.l [100 .mu.l initially to which was added 60 .mu.l of enzyme preparation (3 .mu.l each for 20 cycles)] with a 5.5% variation. The samples were then stored at -20.degree. C.
Manually-Prepared Samples
The steps, which in the above protocol were automated, had been essentially performed manually for two samples, one from Molt4, and one from GM2064 with the following modifications. The initial incubation/denaturing step was performed as in the automated protocol above for eight minutes at 95.degree. C.; however, the first denaturing step, which is repeated in each cycle, was for 2 minutes rather than 2.5 minutes. The annealing step was performed for only two minutes. The enzyme volume was only 2 .mu.l but at a concentration of enzyme of similarly 1 unit of Klenow fragment (0.5 units per .mu.l) so that the final reaction volume was 140 .mu.l per sample.
Dot Hybridization Procedure
Dot blots were prepared containing the automated and hand-processed amplified DNA sequences. .beta.-globin reconstructions were prepared with HaeIII/MaeI-digested pBR:.beta..sup.A (.beta..sup.A is the wild-type allele; Saiki et al., id.) in order to compare the manual and automated samples and estimate the comparative efficiencies of the automated versus manual procedures.
The dot blot procedure is explained in Kafatos et al., "Determination of nucleic acid sequence homologies and relative concentrations by a dot blot hybridization procedure," Nucleic Acids Research, vol. 7, no. 6, pp. 1541-1552 (1979).
Thirty-six nanograms of each of the eight amplified samples and each of the eleven reconstruction samples (the latter ranging from 50-100% at 5% increments as a dilution series standard for the .beta.-globin segment containing the wild-type allele) were diluted to approximately 200 .mu.l of 0.4N NaOH and 25 mM of EDTA (ethylene diaminetetraacetic acid). Each sample was spotted onto a Genatrans nylon membrane (Plasco) which was held in a Bio-Dot clamping device (Bio-Rad Laboratories, Richmond, Calif.). Each well was rinsed with 0.4 ml 20.times. SSPE (1.times. SSPE is 0.18M NaCl, 10 mM NaH.sub.2 PO.sub.4, 1 mM EDTA, pH 7.4). The entire filter was then rinsed in 20.times. SSPE, blotted to dry, and then baked in a vacuum oven for 30 minutes at 80.degree. C.
The filter was prehybridized in 10 ml 3.times. SSPE, 5.times. DET (1.times. DET is 0.02 percent each polyvinylpyrrolidone, Ficoll, and bovine serum albumin; 0.2 mM tris, 0.2 mM EDTA, pH 8.0), 0.5% SDS and 30% formamide and heated at 42.degree. C. for 30 minutes in an incubator oven. Hybridization with 1.0 pmol of the phosphorylated RS06 in 10 ml of the same buffer as tn the prehybridization step was carried out for 60 minutes at 42.degree. C.
The filter was then hybridized with a .sup.32 p-labelled 40-base oligonucleotide probe, RS06, which is complementary to the target sequence, that is , the .beta.-globin segment. (See Saiki et al., id.)
The filter was washed twice in 100 ml of 2.times. SSPE, 0.1% sodium dodecyl sulfate (SDS) at room temperature for ten minutes, and then again in 100 ml of 2.times. SSPE and 0.1% SDS for ten minutes at 55.degree. C.
The filter was then autoradiographed and the blots were compared in intensity to the standard serial dilution reconstructions. The hand- and automated-processed samples containing GM2064 which contains no delta- or beta-globin gone sequences showed no intensity except some background which was removed by a higher stringency wash.
The spots containing the automated amplified samples containing the wild-type allele (.beta..sup.A) from Molt4 and the sickle-cell anemia allele (.beta..sup.s) from SC-1 were similar in intensity to the hand-processed sample containing the Molt4 DNA with the .beta..sup.A alleles.
All four of the samples showing intensity (3 automated and 1 hand-processed) were comparable to the 90% reconstruction.
Other modifications of the above-described embodiments of the invention that are obvious to those of skill in the mechanical and electrical arts and related disciplines are intended to be within the scope of the following claims.
Claims
We claim:
1. A thermal cycling system for performing a polymerase chain reaction amplification protocol comprising multiple cycles of the steps of thermal denaturation of double-stranded DNA, primer hybridization to single-stranded DNA, and template-dependent primer extension by a DNA polymerase, comprising: at least one reaction mixture comprising at least one single- or double-stranded nucleic acid sequence to be amplified, four different deoxyribonucleotides, and a pair of oligodeoxyribonucleotide primers for each said at least one nucleic acid sequence to be amplified, for each said at least one reaction mixture, a heat-conducting reaction chamber, in thermal contact with each said at least one chamber, a variable temperature heating and cooling system, the temperature of said heating and cooling system being computer controllable, and a user-initiable computer controllingly coupled to said heating and cooling system, said computer being programmed to vary the temperature of said heating and cooling system and thereby to vary the temperature of said at least one chamber in accordance with said polymerase chain reaction protocol upon initiation by a user.
2. The thermal cycling system of claim 1, wherein said multiple cycles of the polymerase chain reaction protocol include a repetitive cycle which includes denaturation in the range of from 90.degree. to 105.degree. C. for up to 4 minutes.
3. The thermal cycling system of claim 2, wherein said cycle is repeated at least 15 times.
4. The thermal cycling system of claim 1 comprising a plurality of reaction mixtures, each in a separate reaction chamber, and wherein said heating and cooling system includes a metal block having a plurality of recesses shaped to fit said chambers and fluid flow channels, a temperature-controlled cooling fluid reservoir, and controllable pumping apparatus for pumping a cooling fluid from said cooling fluid reservoir through said channels in said block.
5. The thermal cycling system of claim 4, wherein said multiple cycles of the polymerase chain reaction protocol include a repetitive cycle which includes bring said chamber to a hybridization temperature in the range of from 35.degree. to 65.degree. C. for from 0.5 to 5 minutes, followed by extension product synthesis at a temperature in the range of from 40.degree. to 80.degree. C. for from 0.5 to 40 minutes and then by heating said chamber to a denaturation temperature in the range of from 90.degree. to 105.degree. C. for from 0.5 to 4 minutes.
6. The thermal cycling system of claim 5, wherein said cycle is repeated at least 15 times.
7. The thermal cycling system of claim 4, wherein said multiple cycles of the polymerase chain reaction protocol include a repetitive cycle which includes bringing said chamber to a hybridization temperature in the range of from 35.degree. to 65.degree. C., followed by heating said chamber to a denaturation temperature in the range of from 90.degree. to 105.degree. C. for from 0.5 to 4 minutes.
8. The thermal cycling system of claim 7, wherein said cycle is repeated at least 15 times.
9. The thermal cycling system of claim 4, wherein said heating and cooling system comprises a temperature-controlled heating fluid reservoir and controllable pumping apparatus for pumping a heating fluid from said heating fluid reservoir through said channels in said block.
10. The thermal cycling system of claim 4, further comprising a computer-controlled liquid handler having at least one reagent container and pipettes for transferring reagent from said at least one reagent container into said chamber in response to a transfer control signal.
11. The thermal cycling system of claim 4, wherein said heating and cooling system comprises in electrical heater.
12. The thermal cycling system of claim 1, wherein said heating and cooling system has the capability to cool said at least one reaction mixture to temperatures suitable for reactions utilizing E. coli DNA polymerase I.
13. The thermal cycling system of claim 1, wherein said heating and cooling system has the capability to cool said at least one reaction mixture to temperatures suitable for reactions utilizing Klenow fragment of E. coli DNA polymerase I.
14. The thermal cycling system of claim 1, wherein said steps of hybridization and extension are performed at the same temperature.
15. The thermal cycling system of claim 1, wherein said step of extension is performed at a temperature higher than said step of hybridization.
16. The thermal cycling system of claim 1 comprising a plurality of reaction mixtures and a plurality of reaction chambers, and wherein said heating and cooling system includes a metal block having a plurality of recesses shaped to fit said chambers and a Peltier device.
17. The thermal cycling system of claim 1, wherein said programmed computer is user-programmable in real time.
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