Synthesis of Oligonucleotide Analogs

1. Technical Field of the Invention

The present invention relates to the synthesis of oligonucleotide analogs. More particularly, the invention relates to a novel polymeric disc, wafer or other similarly shaped resin (e.g., planar and non-planar) and a method for its use in solid-phase synthesis.

The present invention permits the rapid production of oligonucleotide analogs, i.e., numerous oligonucleotides differing from one another by only a single base or a small number of bases. The synthesis of analogs according to the present invention can take place at a rapid rate while assuring that the reagents necessary to synthesize the analogs undergo quantitatively complete reactions so as to minimize undesirable side-reaction products which could result in the production of "deletion peptides" or "deletion sequences."

Within recent years, oligonucleotides have been used in crystallographis and biochemical studies of DNA and RNA sequencing and as site-specific mutagens. This and related activity has created an increased need for the chemical synthesis of oligonucleotides and small genes. The present invention greatly simplifies and increases the efficiency of the task of preparing synthetic oligonucleotides.

2. Description of the Prior Art

In the field of peptide chemistry, solid phase peptide synthesis ("SPPS") was introduced by Dr. R. Bruce Merrifield in 1963 when Dr. Merrifield attached a growing peptide chain to a solid support. Merrifield, R. B. (1963) J. Am. Chem. Soc. 85, 2149-2154. The procedures enunciated by Dr. Merrifield for SPPS were as follows: An amino acid corresponding to the C-terminal of the target peptide is covalently attached to an insoluble polymeric support ("the resin"). The next amino acid, with a protected .alpha.-amino acid, is activated and reacted with the resin-bound amino acid to yield an amino-protected dipeptide on the resin. Excess reactants and co-products are removed by filtration and washing. The amino-protecting group is removed by and chain extension is continued with the third and subsequent protected amino acids. After the target protected peptide chain has been built up in this stepwise fashion, all side chain groups are removed and the anchoring bond between the peptide and the resin is cleaved by suitable chemical means thereby releasing the crude peptide product into solution. The desired peptide then undergoes an extensive purification procedure and is then characterized. Kent, S. & Clark-Lewis, I., "Modern Methods for the Chemical Synthesis of Biologically Active Peptides," Division of Biology 147-75, California Institute of Technology, Pasadena, Calif. 91125 U.S.A.; Houghten, R. A., Chang, W. C. & Li, C. H. (1980), Int. J. Pept. Protein Res., 16, 311-320; Houghten, R A., Ostresh, J. M. & Klipstein, F. A. (1984), Eur. J. Biochem., 145, 157-162; Stewart, J. M. & Young, J. D., Solid Phase Peptide Synthesis, Pierce Chemical Company (2d ed. 1984). See, also, Geysen, H. M., 20 Meloen, R. H. & Baretling, S. J. (1984) Proc. Natl. Acad. Sci. USA, 81, 3998-4002; Matthes, H. W. D., Zenke, W. M., Grundstrom, T. Staub, A., Wintzerith, M. & Chambon P., (1984) The EMBO Journal, 3, 801-805.

The resin employed in standard SPPS is known as the "Merrifield resin" and is a polystyrene bead of 100-200 microns in size. The resin typically contains 0.5-2.0% divinylbenzene cross-linkage and contains 0.2 to 0.8 mmole of p-chloromethyl groups per gram resin. The number of p-chloromethyl groups determines the number of individual chains per gram and their ultimate size. The size of the bead allows for a rapid penetration of reagents in SPPS. The percentage of cross-linkage determines the extent to which the resin shrinks and swells during solvent changes. A large shrink-and-swell effect is preferred.

In the field of oligonucleotide chemistry, on the other hand, Dr. Khorana has developed techniques, which were used by others in solution-phase synthesis, for solid-phase synthesis. In doing so, Dr. Khorana eliminated the intensive purification procedures required between each chemical step; the solid-phase procedure only required filtration and rinsing of the solid support with fresh solvent. Solid-phase synthesis permitted chemists to add 15-16 nucleotides per day rather than four or five nucleotides per week.

While the solid phase techniques had revolutionized biomedical research in industry and academia, this procedure has remained essentially unchanged since its inception in the early 1960's. With the explosive pace at which biotechnical research has been advancing in the industrialized nations of the world, substantially more oligonucleotides, particularly analogs, of greater complexity are needed in industry and research than ever before. The ever increasing demand for analog oligonucleotides has been approached in several ways, but no approach thus far, has proven completely satisfactory.

In accordance with the present invention, provided is a novel polymeric disc, wafer or similarly shaped resin for carrying out the synthesis of oligonucleotide analogs via the solid-phase synthesis techniques generally known and described above. The polymeric disc of the present invention may be made out of, for example, five supports presently used in DNA synthesis: polystyrene, silica gel, glass beads, polyamide/kieselguhr and cellulose (e.g., cellulose paper.) If the disc is made of cross-linked polystyrene, preferably there would be 2-5% cross-linkage.

The inventive polymeric disc, which it will be understood as including all suitably shaped and sized resins, whether planar or non-planar, spherical, etc., not merely that which may be thought of as a circular disc, should be sufficiently thin so as to allow for the rapid penetration of reagents to insure that the required reactions may run to completion. The disc of the invention should, preferably, have a thickness of 200-400 .mu.m. Aside from this parameter, i.e., the thickness of the disc, the precise shape of the disc, it should be emphasized, may be any shape having any suitable length or width whatsoever depending upon the requirements of the user.

As part of the present invention, a process for the synthesis of oligonucleotide analogs, using the polymeric resin disc of the invention is further disclosed.

In the Drawing:

The FIGURE outlines the experimental process of solid-phase oligonucleotide synthesis.

The concept of solid-phase peptide synthesis and, as will be explained, as it relates to the present invention may best be understood by reference to the experimental procedure outlined in the FIGURE, wherein X is a reactive group, such as an alkylamine group; L is a labile protecting group; and S is a stable side-chain blocking group to prevent side chain reactions during the oligonucleotide synthesis.

Referring to the FIGURE, a synthetic polymer, such as the polymeric disc of the present invention, would bear reactive groups, X. The nucleotide which will form the 3'-terminal residue of the oligonucleotide to be synthesized is converted to a derivative in which its 5'-hydroxyl group is protected by a labile protecting group, L. Any standard protecting group, such as, for example, the dimethoxytrityl group, may be used in conjunction with the present invention. The foregoing derivative of the 3'-terminal nucleotide is coupled to the reactive polymer. At this point, the repetitive cyclic part of solid-phase synthesis begins. A reagent is applied to the protected polymer to remove the labile blocking group, L, from the nucleotide residue. The reagent employed must not, in any way, harm the link of the 3'-terminal residue to the polymer. Moreover, if the nucleotide attached to the polymer (and all nucleotides in the oligomer to be synthesized) contains a side-chain reactive functional group, that functional group must be blocked by a stable blocking group, S, which will remain completely intact throughout the synthesis, but which can be removed finally to yield the free oligonucleotide. Following removal of the labile protecting group, the next nucleotide is coupled to the polymer by use of a suitable coupling reaction. Again, the 5'-hydroxyl must be protected with the labile group.

This cycle of deprotection and coupling is then repeated with each nucleotide which is to be incorporated into the nucleotide chain. For the deprotection reaction, standard acidolysis methods, such as, a 3% solution of dichloroacetic acid in dichloromethane may be used. Tetrazole may be employed as the activating agent, as well as other suitable agents for use with the present invention. Finally, after the entire blocked oligomer has been assembled on the polymer support, such as the present invention, a different type of reagent, e.g., ammonium hydroxide, is applied to cleave the oligomer from the polymer and allow it to be dissolved. The blocking groups, which have protected side-chain functional groups, must also be removed, and are usually chosen so that they can be removed simultaneously with the cleavage of the oligomer from the resin.

The present invention concerns the polymer support to be employed in the foregoing solid-phase synthesis framework. The support must be insoluble and have satisfactory means of attaching the first nucleotide to it. The polymeric disc of the present invention, i.e., the polymer support, may be made out of those resin materials presently used for solid-phase synthesis when such is carried out with fine bead resins via conventional means. The polymeric disc, which may have any desired shape suitable for the user (e.g., any suitable length or width; planar or non-planar) should, preferably, have a thickness of 200-400 .mu.m. The resin of the present invention may be made out of, for example, polystyrene, silica gel, glass beads, polyamide/kieselguhr and cellulose. If cross-linked polystyrene is to be the material of the resin, the composition of the resin should be at least 1% divinylbenzene; a resin with substantially less than 1% divinylbenzene would be too fragile to be of any use to the chemist.

Additionally, the inventive resin, to be effective, need not rely upon permeation, but may effectively act via a surface reaction. Thus, a hybrid resin may have a strong, inert support, or backing, made of, for example, plastics or nylons (e.g., Nylon-66), or other materials.

The present invention further includes a method for use of the novel polymeric disc. In the synthesis of analogs, discs would be individually tagged. Oligonucleotide synthesis upon the severally tagged discs would take place within one reaction vessel in accordance with known principles of solid-phase synthesis. When the point of deviation in the oligomers is reached, i.e., where the nucleotide(s) which are to differ from one oligonucleotide analog to another in the synthesis process is reached, the discs of the invention can be separated by hand or other procedure (e.g., tongs), reacted separately in different reaction vessels and then, subsequently, again placed in the same reaction vessel to continue or complete the synthesis of the analog chain with those nucleotides generally common to the oligonucleotides.

Finally, a hybrid-type resin, having an inert support as described above, which relies upon a surface reaction, can also be conveniently transferred between reaction vessels with conventional tongs.

The invention will now be more fully described by reference to the following Example. It should, however, be understood that the following Example is for purposes of illustration only and not meant for the purpose of defining the limits or scope of the invention.

The following procedure is suggested for the synthesis of the following three oligonucleotide analogs: ##STR1## wherein, A=adenine;

C=cytosine;

I=inosine;

G=guanine; and

T=thyymine.

Step 1: Place 3 discs into a reaction vessel.

Step 2: Rinse discs as follows:

2.times.20 ml acetonitrile; and,

2.times.20 ml dichloromethane.

Step 3: Derivatize the discs using succinylated 5'-O-dimethoxytrityladenosine in dioxane, pyridine, p-nitrophenol and dicyclohexylcarbodiimide, and let stand overnight.

Step 4: Wash discs extensively with:

2.times.20 ml, N,N dimethylformamide;

2.times.20 ml methanol; and,

2.times.20 ml ether.

Step 5: Deprotect with 20 ml 3% dichloroacetic acid in dichloromethane for 2.times.20 seconds, then rinse two times with the same solution for 5 seconds each.

Step 6: Wash with 5.times.20 ml dichloromethane.

Step 7: Remove Disc #2 and place in second reaction vessel.

Step 8: Dry both vessels under argon gas.

Step 9: Add 1:1 of 0.5M tetrazole and 0.2M 5'-O-dimethoxytritylcytosine-phosphoramidite to Reaction Vessel #1 in a 20-fold excess for the nucleotide. Thereafter, add (1:1) 0.5M tetrazole and 0.2M 5'-O-dimethoxytritylinosine-phosphoramidite to Reaction Vessel #2 in 20-fold for the nucleotide and then react the contents of both reaction vessels (i.e., Reaction Vessels #1 and #2) for 3 minutes.

Step 10: Wash Reaction Vessels #1 and #2 with 20 ml acetonitrile.

Step 11: Re-place Disc #2 into Reaction Vessel #1 and oxidize with 0.1M I.sub.2 solution in approximately 10-20 ml of tetrahydrofuran (THF).

Step 12: Wash with:

2.times.20 ml acetonitrile; and,

2.times.20 ml dichloromethane.

Step 13: Repeat Step Nos. 5, 6 and 8.

Step 14: Add in a 1:1 ratio, 0.5M tetrazole and 0.2M 5'-O-dimethoxytritylcytosine-phosphoramidite in an excess of approximately 20-fold.

Step 15: Repeat Steps Nos. 10-12 and 5-6.

Step 16: Remove Disc #3 and place in Reaction Vessel #2.

Step 17: Repeat Step No. 8.

Step 18: Add in a 1:1 ratio, 0.5M tetrazole and 0.2M of 5'-O-dimethoxytritylguanosine-phosphoramidite to Reaction Vessel #1 in an approximately 20-fold excess. Thereafter, add in a 1:1 ratio, 0.5M tetrazole and 0.2M of 5'-O-dimethoxytritylinosinephosphoramidite to Reaction Vessel #2 in an excess of approximately 20-fold and then react the contents of both reaction vessels for 3 minutes.

Step 19: Repeat Steps Nos. 10-13.

Step 20: Add in a 1:1 ratio 0.5M tetrazole and 0.2M of 5'-O-dimethoxytritylthymosinephosphoramidite to Reaction Vessel No. 1 in an excess of approximately 20-fold and then react the contents of the vessel for 3 minutes.

Step 21: Repeat Steps Nos. 10-13.

Step 22: Cleave oligomers off discs in separate vessels, overnight, using warm ammonium hydroxide.

Step 23: Lyophilize the ammonium hydroxide solution to recover crude oligomers.

While only several embodiments of the present invention have been shown and described, it will be obvious to those skilled in the art that many modifications may be made thereunto without departing from the spirit and scope of the invention.