Vector constructs

[0001] This application claims the benefit under 35 U.S.C. 119 of Great Britain application number GB 0012233.3, filed May 19, 2000.

[0002] The invention relates to improved vector constructs for use in the expression of double-stranded RNA, particularly for use in the expression of double-stranded RNA in vitro and in vivo.

[0003] Since the advent of double-stranded RNA inhibition (RNAi) as a tool for controlling gene expression, as described in WO 99/32619 and WO 00/01846, there has been recognized a need for specialized vectors designed for the production of double-stranded RNA (dsRNA).

[0004] Cloning vectors designed to produce high levels of dsRNA have been previously described by Plaetinck et al. (WO 00/01846) and Timmons et al. Nature, 395:854 (1998). These vectors generally contain a multiple cloning site (MCS) into which target DNA fragments can be cloned flanked by two opposable transcriptional promoters. Essentially, these three components (Promoter 1, MCS and Promoter 2) make up the entire system. In the appropriate expression system, the DNA cloned into the MCS may be transcribed in both directions, leading to the production of two complementary RNA strands.

[0005] A disadvantage of the known systems is that not only the cloned fragment is transcribed. Read-through of the RNA polymerase will result in transcription of the entire vector, and this also in both directions. As only transcription of the cloned DNA fragment will result in active dsRNA for RNAi purposes, transcription of the vector part results in useless, inefficient RNA. More specifically, 80% of these transcripts can be considered as non-specific and thus non-effective.

[0006] The large amounts of non-specific RNA generated by the prior art plasmid and expression systems results in some undesirable side effects. First, in RNAi protocols based on introduction of dsRNA into C. elegans via a food organism such as E. coli which expresses the dsRNA (see WO 00/01846), large RNA strands are considered to be toxic for the food organism. As a result, high amounts of RNA accumulating in E. coli cause a significant part of the population to die.

[0007] Second, and probably more important, is the reduction of inhibition potential. The presence of large amounts of non-specific dsRNA causes a competitive environment for the specified sequences. The potential of the template-specified dsRNA sequences to inhibit the targeted protein expression in, for instance, C. elegans cells is reduced by the presence of these large non-specific regions. Such an inhibition by non-specific dsRNA has also been shown in Drosophila by Tushl et al., Genes & Development 13:3191-3197 (1999). Not only the potential to inhibit gene expression is affected, but also the amount of specific dsRNA produced is limited.

[0008] Third, transcription of the vector backbone part, more particularly transcription of the origin of replication and related structures, results in plasmid instability and plasmid reorganisation, leading to reduced production of dsRNA. This relatively low concentration of effective dsRNA in turn leads to inefficient RNAi.

[0009] To conclude, the previously described vectors have following shortcomings: they are toxic to the feeding organism, a greater proportion of the transcripts produced are non-specific, the inhibitory potential of the dsRNA is reduced by the presence of non-specific regions, a high incidence of plasmid reorganizations and loss of plasmid from the feeding organism. It is therefore an object of the present invention to provide improved vectors for the production of dsRNA which avoid the disadvantages of the prior art vectors.

[0010] Vectors for use in the in vitro synthesis of RNA transcripts, for example the production of RNA probes, have been known and commonly used in the art for some time (see for example F. M. Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (1994); Jendrisak et al, Vectors for in vitro production of RNA copies of either strand of a cloned DNA sequence, U.S. Pat. No. 4,766,072). In standard in vitro transcription protocols the problem of read-through transcription of vector sequences is generally avoided by linearizing the transcription vector at restriction site positioned at the 3′ end of the desired transcript. However, this solution is not appropriate for in vivo transcription or for the production of dsRNA where it is important that the template is transcribed in both directions.

[0011] The inventors now propose a novel solution to the problems encountered with the prior art vectors for the production of dsRNA, based on the use of transcription terminators. Generally the solution consists of the use of at least one transcription terminator operably linked to at least one promoter, wherein the terminator stops the transcription initiated by the promoter. Any DNA fragment inserted between the 3′ end of the promoter and the 5′ end of the terminator will then be transcribed, without the unwanted transcription of the vector backbone. Preferentially the vector consists of two promoters and two terminators, as further described below.

[0012] Therefore, in accordance with a first aspect of the invention there is provided a DNA construct comprising two opposable promoters flanking an inter-promoter region, the construct further comprising at least one transcription terminator positioned transcriptionally downstream of one of the said promoters. In particular, the invention provides for: a DNA construct comprising:

[0013] a) a first promoter and

[0014] b) a second promoter, in which the first and second promoter are in opposite orientation to each other and define:

[0015] c) an inter-promoter region positioned downstream of the 3′ end of the first promoter and downstream of the 3′ end of the second promoter; and which DNA construct further comprises:

[0016] d) at least one cloning site positioned in the inter-promoter region; and

[0017] e) a first transcription terminator, positioned (as seen from the 3′ end of the first promoter) downstream of the first promoter and downstream of the at least one cloning site, wherein the first transcription terminator is operably linked to the first promoter.

[0018] The inter-promoter region can also further be defined as: the DNA region between the 3′ end of the first promoter and the 3′ end of the second promoter, and which is downstream of the first promoter, and which is downstream of the second promoter, and which preferably does not contains the 5′ end of the first promoter and of the second promoter. The opposable first promoter and second promoter drive expression directional from their 5′ ends to their 3′ ends starting transcription downstream of their 3′ ends, thus providing transcription of both strands of any nucleotide sequence(s) present in the inter-promoter region.

[0019] The two promoters present in the DNA construct of the invention may be identical or they may be different and may be of essentially any type. The precise nature of the promoters used in the construct may be dependent on the nature of the expression system in which the construct is expected to function (e.g. prokaryotic vs eukaryotic host cell). Bacteriophage promoters, for example the T7, T3 and SP6 promoters, are preferred for use in the constructs of the invention, since they provide advantages of high level transcription which is dependent only on binding of the appropriate RNA polymerase. Each of these promoters can independently be chosen. The phage promoters can also function in a wide variety of host systems, i.e. both prokaryotic and eukaryotic hosts, provided that the cognate polymerase is present in the host cell.

[0020] The arrangement of two “opposable” promoters flanking an inter-promoter region such that transcription initiation driven by one of the promoters results in transcription of the sense strand of the inter-promoter region and transcription initiation driven by the other promoter results in transcription of the antisense strand of the inter-promoter region is an arrangement well known in the art, for example, in the pGEM7 series of vectors from Promega Corp., Madison Wis., USA.

[0021] The DNA constructs of the invention differ from those of the prior art because of the presence of at least one transcription terminator positioned transcriptionally downstream of one of the promoters. The transcription terminator may be uni- or bi-directional, the choice of uni- vs bi-directional terminators being influenced by the positioning of the terminator(s) within or outside the inter-promoter region, as explained below. The terminator may be of prokaryotic, eukaryotic or phage origin. Bacteriophage terminators, for example T7, T3 and SP6 terminators, are particularly preferred. The only requirement is that the terminator must be capable of causing termination of transcription initiating at the promoter relative to which it is transcriptionally downstream. In practice, these means that the promoter and terminator must form a ‘functional combination’, i.e. the terminator must be functional for the type of RNA polymerase initiating at the promoter. By way of example, a eukaryotic RNA pol II promoter and a eukaryotic RNA pol II terminator would generally form a functional combination. The selection of a functional combination is particularly important where bacteriophage promoters and terminators are to be used in the constructs of the invention, since the phage promoters and terminators are both polymerase-specific. To form a functional combination both the promoter and the terminator should be specific for the same polymerase, e.g. T7 promoter and T7 terminator, T3 promoter and T3 terminator etc.

[0022] In one embodiment, the DNA construct of the invention may comprise a single transcription terminator, positioned (as seen from the 3′ end of the first promoter) downstream of the first promoter and downstream of the at least one cloning site, wherein the first transcription terminator is operably linked to the first promoter, wherein the single transcription terminator is positioned in the inter-promoter region.

[0023] In an alternative arrangement, the DNA construct comprises a single transcription terminator positioned outside of the inter-promoter region. In a still further embodiment, the DNA construct may comprise two transcription terminators, each one of which is positioned transcriptionally downstream of one of the two promoters. In this arrangement, one or both of the terminators may be positioned within the inter-promoter region. These various embodiments of the DNA constructs of the invention will be more fully described below, with reference to the accompanying drawings. The position of a first transcription terminator outside the inter-promoter region may also be further defined as, i.e. such that a first transcription terminator is positioned (as seen from the 3′ end of the first promoter) downstream of the first promoter, downstream of the at least one cloning site, and downstream of the 5′ end of the second promoter.

[0024] The position of a second transcription terminator outside the inter-promoter region may also be further defined as, i.e. such that a second transcription terminator positioned (as seen from the 3′ end of the second promoter) downstream of the second promoter, downstream of the at least one cloning site, and downstream of the 5′ end of the first promoter.

[0025] Moreover, when the terminator is not located in the inter-promoter region, the distance between the 5′ end of the first promoter and 3′ end of the second terminator, or the distance between the 5′ end of the second promoter and the 3′ end of the first terminator is preferably small, i.e. such that the 3′ end of the first transcription terminator is separated from the 5′ end of the second promoter by no more than 2000 nucleotides, preferably no more than 1000 nucleotides, more preferably no more than 500 nucleotides, even more preferably no more than 200 nucleotides, especially preferably no more than 100 nucleotides, more especially preferable no more than 50 nucleotides, even more especially preferably no more than 20 nucleotides, particularly preferably no more than 10 nucleotides, more particularly preferably no more than 6 nucleotides.

[0026] Furthermore, when the second transcription terminator is located outside of the inter-promoter region, preferably the 3′ end of the second transcription terminator is separated from the 5′ end of the first promoter by no more than 2000 nucleotides, preferably no more than 1000 nucleotides, more preferably no more than 500 nucleotides, even more preferably no more than 200 nucleotides, especially preferably no more than 100 nucleotides, more especially preferably no more than 50 nucleotides, even more especially preferably no more than 20 nucleotides, particularly preferably no more than 10 nucleotides, more particularly preferably no more than 6 nucleotides.

[0027] As defined above the term ‘inter-promoter region’ refers to all of the DNA sequence between the two promoters. As explained above, in certain embodiments of the invention the transcription terminator(s) may be sited within the inter-promoter region. The inter-promoter region may, advantageously, comprise a sequence of nucleotides forming a template for dsRNA production. The precise length and nature of this sequence is not material to the invention. The invention further provides DNA constructs in which the inter-promoter region comprises a cloning site. The function of the cloning site is to facilitate insertion of a DNA fragment forming a template for dsRNA production between the two promoters. Thus, the invention provides a series of cloning vectors which are of general use in the construction of template vectors for dsRNA production. Also encompassed within the scope of the invention are vectors derived from the cloning vectors which have a DNA fragment inserted into the cloning site.

[0028] The cloning site may further comprise one or more of the following:

• • [0029] at least one restriction site,(as known in the art), or one or more further restriction sites, e.g. to provide a multiple cloning site(as known in the art),
  • [0030] a stuffer DNA, e.g., flanked by at least two restriction site, such as two BstXI restriction sites, or two XcmI restriction sites,
  • [0031] attR1 and attR2 recombination sites,
  • [0032] a ccdB nucleotide sequence,
  • [0033] a ccdB nucleotide further comprising at least one unique blunt-end restriction site, such as a SrfI restriction site, and/or
  • [0034] a DNA fragment inserted in the at least one cloning site.

[0035] All of the DNA constructs provided by the invention may, advantageously, form part of a replicable cloning vector, such as, for example, a plasmid vector. In addition to the opposable promoters, inter-promoter region and transcription terminator(s), the vector ‘backbone’ may further contain one or more of the general features commonly found in replicable vectors, for example an origin of replication to allow autonomous replication within a host cell and a selective marker, such as an antibiotic resistance gene. The selective marker gene (e.g. the antibiotic resistance gene) may itself contain a promoter and a transcription terminator and it is to be understood that these are completely independent of the promoter and terminator elements required by the invention and are not to be taken into consideration in determining whether a particular vector falls within the scope of the invention.

[0036] DNA constructs according to the invention may be easily be constructed from the component sequence elements using standard recombinant techniques well known in the art and described, for example, in F. M. Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (1994), as will be appreciated by one skilled in the art from the following detailed description of the invention and the accompanying Examples.

[0037] There follows a detailed description of DNA constructs according to the invention, with reference to the following drawings.

[0056] Referring to the Drawings, FIG. 1(a) schematically illustrates a first DNA construct according to the invention which is a plasmid vector comprising two opposable promoters; a first promoter (a) and a second promoter (b) flanking an inter-promoter region (c), which inter-promoter region is downstream of the 3′ of the first promoter, and down stream of the 3′ end of the second promoter. The first promoter and the second promoter may be identical or different. This embodiment comprises a first transcription terminator (e) and a second transcription terminator (f), both of which are positioned within the inter-promoter region. In this embodiment, the first terminator and the second terminator are preferentially uni-directional terminators.

[0057] A DNA fragment may be inserted in the at least one cloning site (d). Such DNA fragment is subject to transcription directed by the first promoter (a) and the second promoter (b) (i.e. transcription of both strands), resulting in the generation of two RNA fragments which may combine to form double-stranded RNA of the inserted DNA fragment (both in vitro and in vivo).

[0058] Any desired DNA sequence, such as a genomic DNA sequence, or a cDNA sequence or any other coding sequence, may be inserted in the at least one cloning site. Without being limited to any specific explanation, it is assumed that when (a) and (e) form a functional combination, RNA polymerase which initiates transcription at (a) will transcribe the inter-promoter region including the at least cloning site and the DNA fragment inserted in the at least cloning site and will be terminated when it reaches (e). Similarly, RNA polymerase which initiates transcription at (b) will transcribe the inter-promoter region including the at least one cloning site and the DNA fragment inserted in the at least one cloning site and will terminate when it reaches (f). The terminators cause the RNA polymerase to pause, stop transcription and fall off the template. This prevents the unlimited transcription of the vector backbone, and reduces the unspecific transcription of non-essential DNA.

[0059] The inter-promoter region further comprises a sequence of nucleotides corresponding to a target for double-stranded RNA inhibition. This sequence is designated ‘TF’=for target fragment. It is this sequence which, when transcribed into dsRNA, will be responsible for specific double-stranded RNA inhibition of a target gene. The target fragment may be formed from a fragment of genomic DNA or cDNA from the target gene. Its precise length and nucleotide sequence are not material to the invention.

[0060] In the arrangement shown in FIG. 1(a) the two terminators are positioned on either side of the TF within the inter-promoter region. Each of the terminators is positioned transcriptionally downstream of one of the promoters, the fist terminator (e) is transcriptionally downstream of first promoter (a) and the second terminator (f) is transcriptionally downstream of the second promoter (b). Assuming that (a) and (e) form a functional combination, as described above, RNA polymerase which initiates transcription at a) will transcribe the inter-promoter region up to and including TF and will be terminated when it reaches (e). Similarly, RNA polymerase which initiates transcription at (b) will transcribe the inter-promoter region up to and including TF on the opposite strand and will terminate when it reaches (f). The terminators cause the RNA polymerase to pause, stop transcription and fall off the template. This prevents the unlimited transcription of the vector backbone, and reduces the unspecific transcription of non-essential DNA.

[0061] The transcripts generated from this vector may, depending on the precise placement of the terminators in the vector, be almost completely specific dsRNAs corresponding to the TF region. Through the direct placement of the terminator sequences at the downstream end of the TF region on both sides of the inserted DNA fragment, the amount of material transcribed is completely reduced to the template-specified sequences. Therefore, a higher amount of specific dsRNA is obtained. Furthermore the constructs are now also more stable, due to the non-transcription of the vector backbone. The latter characteristic (stability), combined with the now relatively higher specific transcription rate, provides a system adapted to synthesize higher amounts of specific short dsRNA strands. This proportionally higher amount of transcript, resulting in high concentrations of specific dsRNA, enhances the inhibitory effect in RNAi protocols. In RNAi protocols based on expression of dsRNA in a food organism, toxicity for the feeding organisms due to high RNA expression is brought to a minimal level by use of this vector.

[0062] A specific example of a vector of the type illustrated in FIG. 1(a), considered by the inventors to be the optimal arrangement for RNAi applications, is plasmid pGN9 described in the accompanying Examples. The transcriptional terminators used in pGN9 are T7 RNA polymerase specific terminators, since the vector contains two opposable T7 promoters. However, other systems could be used such as an expression system based on the T3 or SP6 promoter, terminator and polymerase or other prokaryotic or eukaryotic promoters and terminators.

[0063] FIG. 1(b) illustrates schematically a further DNA construct according to the invention which is a plasmid vector comprising two opposable promoters (a) and (b) flanking an inter-promoter region (c). This vector also comprises two transcription terminators (e) and (f) but in this arrangement the two terminators are positioned outside of the inter-promoter region, in fact the terminator elements now flank the two promoters. The arrangement is such that (e) is transcriptionally downstream of (a) whilst (f) is transcriptionally downstream of (b). Here again (e) terminates the transcription initiated by (a), whilst (f) terminates the transcription initiated by promoter (b). Placement of the terminators outside of (d) allows the use of bi-directional terminators as well as uni-directional terminators, in contrast to the arrangement in FIG. 1(a) where uni-directional terminators are preferred because of the placement of the terminators between the promoters. A number of bi-directional terminators which could be used in accordance with the invention are known in the art. Generally these are observed to be polymerase non-specific.

[0064] The embodiment shown in FIG. 1(b) provides essentially the same advantages as that shown in FIG. 1(a) over the prior art vectors for dsRNA production. The vector shown in FIG. 1(b) will lead to the production of transcripts which are slightly longer, including the promoter regions. This relatively small difference in the length of the transcript and hence the formed dsRNA will not severely affect the efficacy in an RNAi system.

[0065] The position of the terminators and promoter in the example as shown in FIG. 1(b) are preferably placed at close proximity, such that the 5′ end of the promoters are separated from the 3′ end of the transcription terminators by no more than 2000 nucleotides, preferably no more than 1000 nucleotides, more preferably no more than 500 nucleotides, even more preferably no more than 200 nucleotides, especially preferably no more than 100 nucleotides, more especially preferably no more than 50 nucleotides, even more especially preferably no more than 20 nucleotides, particularly preferably no more than 10 nucleotides, more particularly preferably no more than 6 nucleotides.

[0066] FIG. 1(c) illustrates schematically a further DNA construct according to the invention which is a plasmid vector comprising two opposable promoters (a) and (b) flanking an inter-promoter region (c). In this embodiment one terminator (in this case (f)) is positioned within the (c) and the other (e) is positioned outside (c). Again, (e) terminates transcription initiated by (a) and (f) terminates transcription initiated by (b). This arrangement may provide a useful solution to the problem of one of the terminators interfering with polymerase activity in the other direction (e.g. (f) interferes with (b) initiated transcription). This vector essentially provides the same advantages as the vector variations shown in FIG. 1(a) and FIG. 1(b) over the prior art. The relatively small difference in the length of the transcript due to the transcription of one of the promoters will not significantly affect the efficacy in RNAi systems. This more particularly the case when the terminator that is located outside of the inter-promoter region (c) is at close proximity of the promoter, as defined above.

[0067] FIGS. 1(d) and 1(e) illustrate schematically two further DNA constructs according to the invention which are both plasmid vectors comprising two opposable promoters (a) and (b) flanking an inter-promoter region (c). These embodiments comprise a single terminator only. In the arrangement shown in FIG. 1(d) a single terminator (e) which terminates transcription from (a) is placed outside of (c). The placement of the terminator outside of the inter-promoter region allows the use of both a bi-directional terminator or a uni-directional terminator in this system. In the embodiment shown in FIG. 1(d), (e) is placed within the (c) and should therefore preferably be a uni-directional terminator.

[0068] Further embodiments of the DNA construct according to the invention are illustrated schematically in FIGS. 2(b) to 2(e).

[0069] These embodiments are all plasmid cloning vectors, based upon the optimal arrangement of promoters and terminators shown in FIG. 1(a), and described above, containing cloning sites to facilitate the insertion of a DNA fragment into the at least one cloning site.

[0070] These embodiments are all plasmid cloning vectors, based upon the optimal arrangement of promoters and terminators shown in FIG. 1(a), containing cloning sites to facilitate the insertion of a target DNA fragment into the inter-promoter region.

[0071] FIG. 2(a), which is a schematic representation of a prior art cloning vector, is included for comparison purposes. This vector comprises two opposable promoters (a) and (b), which may be identical or different, flanking a multi-cloning site (MCS).

[0072] FIG. 2(b) illustrates a first type of plasmid cloning vector according to the invention. The vector contains a first opposable promoter (a) and a second opposable promoter (b) flanking an inter-promoter region. The inter-promoter region can further be defined as: the DNA region between the 3′ end of the first promoter and the 3′ end of the second promoter, and which is downstream of the first promoter, and which is downstream of the second promoter, and which preferably does not contain the 5′ end of the first promoter and of the second promoter. The inter-promoter region further comprises terminators (e) and (f) flanking a multi-cloning site MCS. The MCS comprises at least one individual restriction site, and preferably more than one restriction site as known in the art, any of which may be used for insertion of a DNA fragment.

[0073] FIG. 2(c) illustrates a further type of plasmid cloning vector according to the invention. This vector again contains opposable promoters (a) and (b) flanking an inter-promoter region comprising terminators (e) and (f). In this embodiment, (a) and (b) flank a cloning site which is adapted for facilitated cloning of PCR fragments, comprising a stuffer DNA flanked by two identical restriction sites, in this case BstXI sites. The specific sequence of the stuffer DNA is not essential, provided that said stuffer DNA does not interfere with the desired effect and/or the desired activity of the DNA constructs of the invention. A specific example of a vector according to this aspect of the invention described herein is plasmid pGN29.

[0074] The cloning of PCR products using BstXI recognition sites and BstXI adaptors is generally known in the art. The BstXI adaptors are commercially obtained, such as from Invitrogen (Groningen, the Netherlands). These adaptors are non-palindromic adapters designed for easier and efficient cloning of PCR products into vectors. These use of these adaptors reduces the concatamerization of adapters or insert DNA by having non-complementary (CACA) overhangs. The stuffer DNA is included merely to allow easy differentiation between BstXI cut and uncut vector on the basis of size. Its precise length and sequence are not of importance.

[0075] FIG. 2(d) illustrates a further type of plasmid cloning vector according to the invention. This vector again contains opposable promoters (a) and (b) flanking an inter-promoter region comprising terminators (e) and (f). In this embodiment, (a) and (b) flank a cloning site which facilitates “High Throughput” cloning based on homologous recombination rather than restriction enzyme digestion and ligation. As shown schematically in FIG. 2(d), the cloning site comprises attR1 and attR2 recombination sites from bacteriophage lambda flanking a gene which is lethal to E. coli, in this case the ccdB gene.

[0076] An alternative cloning method of DNA fragments into this vector,(not shown in FIG. 2(d)), consists of a variant of this vector, wherein the ccdB DNA sequence further comprises at least one unique restriction site, preferably the at least unique restriction site is a blunt-end restriction site, such as a SrfI restriction site. Insertion of a DNA fragment in the at least one unique restriction site, results in inactivation of the ccdB gene, and hence in inactivation of the lethal ccdB gene product.

[0077] A further variant of a vector a shown in FIG. 2(d) in which the attR1 and the attR2 are not present. Such a vector comprises at least one cloning site, said at least one cloning site consisting of a ccdB sequence, said ccdB sequence further comprising at least one unique restriction site, preferably the at least unique restriction site is a blunt-end restriction site, such as a SrfI restriction site. Insertion of a DNA fragment in the at least one unique restriction site, results in inactivation of the ccdB gene, and hence in inactivation of the lethal ccdB gene product.

[0078] These cloning sites comprising the ccdB nucleotide sequence and/or the attR sites (R1 and/or R2) are derived from the Gateway™ cloning system commercially available from Life Technologies, Inc. The Gateway™ cloning system has been extensively described by Hartley et al. in WO 96/40724 (PCT/US96/10082). A specific example of a vector according to this aspect of the invention described herein is pGN39.

[0079] FIGS. 2(e) and 2(f) illustrate a still further type of plasmid cloning vector according to the invention. This vector again contains opposable promoters (a) and (b) flanking an inter-promoter region (c) comprising terminators (e) and (f). In the embodiment shown in FIG. 2(e), terminators (e) and (f) flank a cloning site which facilitates “high throughput” cloning of PCR products by TA™ cloning. This cloning site comprises a stuffer DNA flanked by two identical restriction sites for an enzyme which generates overhanging T nucleotides. In this case the restriction sites are XcmI sites, but other sites which are cleaved to generate overhanging T nucleotides could be used with equivalent effect. The overhanging T nucleotides facilitate cloning of PCR products which have a overhanging A nucleotide. This principle is known as TA™ cloning. The cut vector with overhanging T nucleotides can be “topomerized” to generate a cloning vector of the type shown schematically in FIG. 2(f), by linking the enzyme topoisomerase to the overhanging T nucleotides. The resulting vector also facilitates the cloning of PCR products by the principle known as TOPO™ cloning.

[0080] Both the TOPO™ and TA™ cloning systems, although not for the vectors described in this invention, are commercially available from Invitrogen. The TOPO™ cloning system has extensively been described by Shuman in WO 96/19497 (PCT/US95/16099). The TA™ cloning system has extensively been described by Hernstadt et al. in WO 92/06189 (PCT/US91/07147).

[0081] It will be readily appreciated by the skilled reader that whilst FIGS. 2(b)-2(f) illustrate the inclusion of different cloning sites into a vector of the type illustrated in FIG. 1(a), these cloning sites could be included into any of the DNA constructs of the invention, including those illustrated schematically in FIGS. 1(b) to 1(e)

[0082] As aforementioned, a major application of the DNA constructs/vectors of the invention is in the production of double stranded RNA for use in RNAi technology. In particular, the constructs are useful in in vivo RNAi protocols in the nematode worm C. elegans.

[0083] In C. elegans, RNAi has traditionally been performed by injection dsRNA into the worm. Fire et al. describes these methods extensively in International Application No. WO 99/32619. In short, both strands of RNA are produced in vitro using commercially available in vitro transcription kits. Both strands of RNA are allowed to form dsRNA, after which the dsRNA is injected into C. elegans.

[0084] The new vector system developed by the present inventors is a drastic improvement on this traditional method. First, the RNA can be produced in one step, for instance by using two identical promoters such as in the vector pGN9. Second, and more important, due to the presence of terminators the transcripts, and hence the formed dsRNA, will be more specific as only the cloned target fragment will be transcribed. This will result in a more efficient RNAi.

[0085] A further method to perform RNAi experiments in C. elegans has been described by Plaetinck et al. in WO 00/01846. In this method C. elegans worms are fed with bacteria which produce dsRNA. The dsRNA passes the gut barrier of the worm and induces the same RNAi as if the dsRNA has been injected. For these experiments, the preferred E. coli strain is HT115 (DE3), and the preferred C. elegans strain is nuc-1;gun-1. The improved vectors provided by the invention also improve the efficiency of RNAi in this method, as shown in the example below, as only effective dsRNA is produced.

[0086] Another method to perform RNAi has also been described by Plaetinck et al. in WO 00/01846. In short, this method is based on the production of dsRNA in the worm itself. This can be done by using worm promoters in the described vectors, or by using a transgenic worm expressing a polymerase specific for non-C. elegans promoters present in the vector, such that this polymerase drives transcription of the dsRNA. The promoters will preferentially be selected from the known bacteriophage RNA promoters, such as T7 or T3 or SP6 RNA promoters, which provide the advantage of a high level of transcription dependent only on the binding of the cognate polymerase.

[0087] Plasmid vector DNA can be introduced into the worm by several methods. First, the DNA can be introduced by the traditional injection method (Methods in Cell Biology, Vol 48, C. elegans Modern Biological Analysis of an organism, ed. by Epstein and Shakes). Second, the DNA can be introduced by DNA feeding. As has been shown by Plaetinck et al. in WO 00/01846, plasmid DNA can be introduced into the worm by feeding the worm with an E. coli strain that harbors the plasmid. Preferentially the E. coli strain is OP50, or MC1061 or HT115 (DE3) but any other strain would suit for this purpose. The C. elegans strain is preferentially a nuc-1 mutant strain or a nuc-1; gun-1 strain. The plasmid DNA from the E. coli passes the gut barrier and is introduced into the nematode, resulting in the expression of dsRNA. As with the other RNAi methods described above, the use of the new vector system will enhance the RNAi by the production of only specific dsRNA.

[0088] The invention will be further understood with reference to the following experimental Examples, together with FIGS. 3-17.

[0089] The starting point for construction of the vectors exemplified herein was plasmid pGN1. This plasmid, described in the applicant's co-pending International Application No. WO 00/01846, contains two opposable T7 promoters flanking a multi-cloning site.

[0090] Vector construction was carried out according to standard molecular biology techniques known in the art and described, for example, in F. M. Ausubel et al. (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (1994).

1) Construction of pGN9

[0091] pGN1 was first digested with restriction enzymes EcoRI and KpnI. Oligonucleotides oGN27 (SEQ ID NO:3) and oGN28 (SE ID NO:4) (FIG. 7) were annealed to generate a double stranded fragment which was then ligated into the EcoRI/KpnI cut vector. The resulting plasmid was re-digested with XbaI and HindIII. Oligonucleotides oGN29 (SEQ ID NO:5) and oGN30 (SEQ ID NO:6) were annealed to generate a double-stranded fragment which was then annealed into the XbaI/HindIII cut vector. The resulting vector was designated pGN9 (FIGS. 4 and 10; SEQ ID NO:8).

2) Construction of Further Cloning Vectors

[0092] pGN29 (FIG. 9(a); FIG. 11; SEQ ID NO:9) was generated by replacing the MCS in pGN9 with a stuffer DNA flanked by BstXI sites. BstXI adapters are commercially available from Invitrogen (Groningen, the Netherlands).

[0093] pGN39 (FIG. 9(b); FIG. 12; SEQ ID NO:39) was generated by following steps; pGN29 was digested with BsTXI. BstXI adapters (Invitrogen, Groningen, The Netherlands) were ligated to Cassette A provided by the GATEWAY™ system (Life Technologies, Inc.). Cassette A contains attR1, CmR, ccda, ccdB, attR2. The Cassette A with the adapters were then ligated into the digested pGN29, resulting in pGN39A. pGN39A contains a unique SrfI site in the ccdB gene.

[0094] The TopoRNAi vector (FIG. 9(c); FIG. 13; SEQ ID NO:11) was generated in the following way; pGN29 was digested with BstXI. Using PCR with the primers oGN103 (SEQ ID NO:14) and oGN104 (SEQ ID NO:15) and template pCDM8 (Invitrogen, Groningen, The Netherlands), a stuffer was generated (SEQ ID NO: 20) which includes XcmI sites. Onto the PCR product, BstXI adapters were ligated, and the resulting ligation product was ligated in the BstXI digested pGN29 vector resulting in the TopoRNAi vector.

[0095]

	oGN103 (SEQ ID NO:14):
	5′ TACCAAGGCTAGCATGGTTTATCACTGATAAGTTGG 3′
	oGN104 (SEQ ID NO:15):
	5′ TACCAAGGCTAGCATGGGCCTGCCTGAAGGCTGC 3′

[0096] pGN49A (SEQ ID NO:12) was constructed to insert an additional unique non-blunt restriction site and to delete the CmR gene from pGN39. Overlap PCR was used. A first PCR was performed with primers oGN126 (SEQ ID NO:16)and oGN127 (SEQ ID NO:17) and PGN39A as template. Using primers oGN128 (SEQ ID NO:18) and OGN129 (SEQ ID NO:19) and the same template a second fragment was generated. Overlap PCR using the resulting fragments and primers oGN126P and oGN129P resulted in a final PCR product. To this final PCR product, BstXI adapters were ligated, and the ligation product was ligated into pGN29 digested with BstXI. The resulting vector was designated pGN49A.

[0097] A control vector was generated to test the efficiency of the pGN49A cloning vector, such vector should contain the T7 promoters, but not the T7 terminators. For this, the XbaI insert of pGN49A was isolated and cloned in pGN1 digested with the same restriction enzyme. The resulting vector was designated pGN59A (SEQ ID NO:13).

[0098]

oGN126 (SEQ ID NO:16):
pGATCTGGATCCGGCTTACTAAAAGCCAGATAACAGTATGC
oGN127 (SEQ ID NO:17):
GGAGACTTTATCGCTTAAGAGACGTGCACTGGCCAGGGGGATCACC
oGN128 (SEQ ID NO:18):
CCAGTGCACGTCTCTTAAGCGATAAAGTCTCCCGTGAACTTTACCCGGTGG
oGN129 (SEQ ID NO:19)
pGCTGTGTATAAGGGAGCCTGACATTTATATTCCCCAG

[0099] This experiment was designed to illustrate the improved efficiency of the improved vectors of this invention in double-stranded RNA inhibition, as compared to the vectors known from the prior art. A significant increase on the efficacy of the system could be expected, as more effective dsRNA was produced and hence RNAi performed better. The experimental system for this proof of concept experiment was to measure C. elegans rescue at 25° C. in nuc-1/pha-1(e2123)ts C. elegans mutants by RNAi of sup35 using dsRNA feeding of pGN-2 (−terminator) and pGN-12 (+terminator), with PGN-1 (empty vector) as a control and dilutor. The pha-1 ts/sup-35 mutation has extensively been described by Schnabel in WO 99/49066.

[0100] The nuc-1 mutation in C. elegans provides for a C. elegans strain exhibiting better uptake abilities, such as the uptake of the dsRNA complexes than wild type C. elegans. This mutant is deleted in the major DNAse enzymes, and inventors have proven in earlier co-pending applications that this C. elegans strain results in enhanced RNAi by feeding the nematode with dsRNAs.

[0101] The pha-1(e2123)ts mutation provides a mutant C. elegans strain with a phenotype of survival at 15° C. and lethality at 25° C. This lethality is suppressible by the inhibition of sup-35 expression. RNAi of sup-35 should thus facilitate the rescue of pha-1(e2123)ts at 25° C. The vectors of the present invention, when expressing dsRNA from sup-35, should increase the efficacy of sup-35 RNAi in rescuing pha-1(e2123)ts mutants at 25° C., compared to vectors that do not contain the terminators.

[0102] Vector pGN1 was used as empty vector. Vector pGN2 (−terminator) is a vector harboring sup-35 DNA and expressing sup-35 dsRNA when introduced in the appropriate host, the vector has no transcriptional terminators inserted. Vector pGN12 (+terminator) is a vector as described above, containing the transcriptional terminators, and hence resulting in improved dsRNA production when introduced into an appropriate host. Thus, this vector has two unidirectional transcriptional terminators, both placed inside of the inter-promoter region, and flanking the sup-35 fragment. Use of the latter vector was expected to increase the efficacy of the system, here meaning a better rescue (survival) of pha-1(e2123)ts mutants at 25° C.

Experimental Conditions

[0103] 12-well micro-titer plates were filled with approximately 2 ml of NGM agar per well. (1 liter of NGM agar: 15 g Agar, 1 g peptone, 3 g NaCl, 1 ml cholesterol solution (5 mg/ml in EtOH), with sterile addition after autoclaving of 9.5 ml 0.1M CaCl₂, 9.5 ml 0.1 ml MgSO₄, 25 ml 1M KH₂PO₄/K₂HPO₄ buffer pH 6, ampicillin (100 μg/l), 5 ml 0,1 M IPTG and 5 ml nystatin solution (dissolved 10 mg/ml in 1:1 EtOH:CH₃COONH₄ 7.5 M)

[0104] The dried plates were spotted with approximately 50 μl of an overnight culture of bacteria HT115 (DE3) (Fire A, Carnegie Institution, Baltimore, Md.) transformed with the plasmids. Individual nematodes at the L4 growth stage were then placed in single wells at day 1. In each well 1 nematode was placed (P1). At day two, the P1 nematodes were placed to a new well and left to incubate for a day. The same procedure was repeated at day 3. All plates were further incubated at 25° C. to allow offspring to be formed. Sup35 RNAi induced survival (rescue) as was measured by counting the offspring.

Results

[0105] RNAi experiment in C. elegans nuc-1/pha-1(e2123)ts mutants by feeding with E. coli expressing sup-35 dsRNA.

Set Up:

• [0106] pGN1 as control
• [0107] pGN2 (sup 35−Term.)
  • [0108] pGN12 (sup 35+Term.)
• [0109] pGN2+pGN1 dilutions ½, ¼, ⅛, 1/16, 1/32
  • [0110] pGN12+pGN1 dilutions ½, ¼, ⅛, 1/16, 1/32
    Conditions:
• [0111] Incubation temperature 25° C.
  Readout:

[0112]

Count offspring (adult hermaphrodites)
pGN1 (control)
Day 1	0	0	0	0
Day 2	0	0	0	0
Day 3	0	0	0	0
pGN2 (undiluted)	pGN12 (undiluted)
Day 1	12	4	48	32	Day 1	16	29	37	14
Day 2	24	23	80	85	Day 2	27	22	57	2
Day 3	5	0	9	16	Day 3	1	2	4	1
pGN 2 + 1, ½ dilution	pGN 12 + 1, ½ dilution
Day 1	0	7	0	2	Day 1	22	28	103	61
Day 2	9	10	0	3	Day 2	36	45	53	40
Day 3	0	2	0	0	Day 3	3	3	25	1
pGN 2 + 1, ¼ dilution	pGN 12 + 1, ¼ dilution
Day 1	28	23	0	0	Day 1	*	6	36	5
Day 2	6	3	0	0	Day 2		24	55	3
Day 3	0	0	0	0	Day 3
pGN 2 + 1, ⅛ dilution	pGN 12 + 1, ⅛ dilution
Day 1	0	0	4	0	Day 1	31	12	16	38
Day 2	0	0	11	0	Day 2	4	5	37	4
Day 3	0	0	0	0	Day 3	0	0	2	1
pGN 2 + 1, 1/16 dilution	pGN 12 + 1, 1/16 dilution
Day 1	0	0	0	0	Day 1	1	0	0	0
Day 2	0	0	0	1	Day 2	2	0	0	1
				little
Day 3	0	0	0	0	Day 3	0	1	1	1
pGN 2 + 1, 1/32 dilution	pGN 12 + 1, 1/32 dilution
Day 1	0	0	0	0	Day 1	0	0	1	0
Day 2	0	0	0	0	Day 2	0	L2	3	0
Day 3	0	0	0	0	Day 3	2	0	L3-L4	0
* mother died

Conclusions

[0113] As expected, worms fed by bacteria harboring pGN1, did not result in the viable offspring, due to the lethal effect of the pha-1 mutation at this temperature.

[0114] Feeding the nematodes with E. coli harboring pGN2 or pGN12 both result in viable offspring. This is due to the feeding of the worm with dsRNA from sup-35. The remarkable difference between the two feeding experiments can be seen in the dilution series. When diluting the bacteria harboring pGN2 with bacteria harboring pGN1, the number of offspring diminishes drastically, even at a low dilution of one to two. This dilution series indicates that high levels of dsRNA are needed to have a proper RNAi induction. In the feeding experiment with bacteria harboring pGN12, significant offspring is still observed at a dilution of one to eight. This indicates that in the bacteria harboring pGN12, much more effective dsRNA is formed.

[0115] This experiment clearly shows that the addition of terminator sequences in vectors to express dsRNA as described above provide a significant advantage in the generation of RNAi.

[0116] Three different genes have been cloned in the vectors pGN49A and pGN59A. The cloning was performed by amplifying the gene fragments with PfuI DNA polymerase producing blunt ends, facilitating cloning in these vectors. These PCR fragments were cloned into the vectors digested with SrfI. Correct fragment insertion of the clones was checked by PCR. The fragments are chosen such that ds expression and RNAi results in a lethal phenotype of the offspring. This procedure allows fast and easy comparison of the efficiency of the two vectors pGN49 and pGN59 in RNAi.

[0117]

	plasmid	Gene (acedb)	Vector backbone
	pGW5	B0511.8	pGN49A
	pGW9	C01G8.7	pGN49A
	pGW11	C47B2.3	pGN49A
	pGW17	B0511.8	pGN59A
	pGW21	C01G8.7	pGN59A
	pGW23	C47B2.3	pGN59A

[0118] All the plasmids (pGW-series)are transformed in E. coli AB301-105 (DE3) bacteria by standard methodology. The bacteria are then grown in LB/amp at 37° C. for 14-18 h. These cultures were centrifuged and the bacterial pellet dissolved in S-complete buffer containing 1 mM IPTG and 100 μg/μl ampicillin.

[0119] In 96 well plates containing 100 μl S-complete (containing 1 mM IPTG and 100 μg/μl ampicillin final concentration) and 10 μl of bacteria solution, 3 nematodes were added at each well, the nematodes were at the L1 growth stage.

[0120] The plates were incubated at 25° C. for 5-6 days. Each day the plates were inspected for development of the larvae and the production of F1 offspring.

Results

[0121] The RNAi was performed in eight-fold for each constructed plasmid. The results show that when T7 terminators are inserted into the vector backbone, the expected phenotype gives a 100% occurrence. When T7 terminators are not used the reproducibility can decrease up to 50%. As in the previous experiment, the results show that the addition of terminators significantly enhances RNAi performance.

[0122]

	DNA fragment
	B0511.8	B0511.8	C01G8.7	C01G8.7	C47B2.3	C47B2.3
Vector	pGN49A	pGN59A	PGN49A	pGN59A	pGN49A	pGN59A
Resulting	PGW5	PGW17	PGW9	PGW21	PGW11	PGW23
plasmid
Percentage	100	75	100	87.5	100	50
lethal
Percentage	0	25	0	12.5	0	50
offspring

[0123]

PCR fragment generated by the primers oGN103 and
oGN104 on template pCDM8 (SEQ ID NO:20)
	taccaaggct agcatggttt atcactgata agttgg
	ataagttggt ggacatatta tgtttatcag tgataaagtg tcaagcatga
	caaagttgca gccgaataca gtgatccgtg ccggccctgg actgttgaac
	gaggtcggcg tagacggtct gacgacacgc aaactggcgg aacggttggg
	ggtgcagcag ccggcgcttt actggcactt caggaacaag cgggcgctgc
	tcgacgcact ggccgaagcc atgctggcgg agaatcatac gcttcggtgc
	cgagagccga cgacgactgg cgctcatttc tgatcgggaa tcccgcagct
	tcaggcaggc ccatgctagc cttggtacca gcacaatgg

[0124]

Overlap PCR Fragment, which was used to generate
pGN49A (SEQ ID NO:21)
gatctggatccggcttactaaaagccagataacagtatgcgtatttgcgc
gctgatttttgcggtataagaatatatactgatatgtatacccgaagtat
gtcaaaaagaggtgtgctatgaagcagcgtattacagtgacagttgacag
cgacagctatcagttgctcaaggcatatatgatgtcaatatctccggtct
ggtaagcacaaccatgcagaatgaagcccgtcgtctgcgtgccgaacgct
ggaaagcggaaaatcaggaagggatggctgaggtcgcccggtttattgaa
atgaacggctcttttgctgacgagaacagggactggtgaaatgcagttta
aggtttacacctataaaagagagagccgttatcgtctgtttgtggatgta
cagagtgatattattgacacgcccgggcgacggatggtgatccccctggc
cagtgcacgtctcttaagcgataaagtctcccgtgaactttacccggtgg
tgcatatcggggatgaaagctggcgcatgatgaccaccgatatggccagt
gtgccggtctccgttatcggggaagaagtggctgatctcagccaccgcga
aaatgacatcaaaaacgccattaacctgatgttctggggaatataaatgt
caggctcccttatacacagc

[0125] Other aspects of the invention will be clear to the skilled artisan and need not be repeated here. Each reference or publication cited herein is incorporated by reference in its entirety.

[0126] The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, it being recognized that various modifications are possible within the scope of the invention.