DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
Acknowledgement is made of Applicants’ claim for benefit to prior filed US Provisional Application 62/461689, filed on 02/21/2017. This application is a continuation of application 16/487223 filed on 08/20/2019 (now abandoned), which is a 371 of PCT/US18/19056 filed on 02/21/2018.
Information Disclosure Statement
The IDS filed 03/03/2023 has been considered by the Examiner.
Status of Claims
Claims 1-34 are under examination.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-9, 13-18, and 23-34 are rejected under 35 U.S.C. 103 as being unpatentable over Boyne et al. (WO 2016/126747 Al) as evidenced by Li et al. (2012).
Regarding claim 1, Boyne et al. teach a polynucleotide cassette for regulation of expression of a target gene comprising a riboswitch (page 1, paragraph 0001). Boyne et al. teach the riboswitch comprises an effector stem loop and an aptamer (page 1, paragraph 0001). Boyne et al. teach the aptamer (sensor) and effector stem loop are linked by a polynucleotide linker (page 13, paragraph 0056). Boyne et al. teach the polynucleotide linker forms an RNA stem (page 13, paragraph 0056). Boyne et al. teach the riboswitches are used for targeted regulation (cover page, abstract). Boyne et al. teach the method provides improved safety of a gene therapy treatment by allowing the target gene to be off in the absence of the ligand (page 23, paragraph 0097). Boyne et al. teach linking the lower stem of aptamer directly to the hairpin stem and further teach the stem needs to be an optimal length to form a stable stem structure (Fig. 4c, DHFR Theo1). Boyne et al. teach if the stem is too long, it may form a stable structure in the absence of aptamer/ligand binding, while if it is too short it may never form a stable stem, even when the ligand is present (page 14, paragraph 0059). Boyne et al. teach the aptamer sequences were attached to the stem of a hairpin structure that embeds the intronic portion of the DHFR 5' ss and its complementary sequence (page 35, paragraph 00152). Boyne et al. teach the expression construct includes a polyadenylation signal (page 45, paragraph 00212). Boyne et al. further teach a conformational change in aptamer triggered by ligand binding brings together the DHFR 5' ss and its complementary sequence and the complementary sequence supports stable stem formation (page 35, paragraph 00152). Boyne et al. teach the aptamer can have an additional stem portion which comprises a sequence from the aptamer stem (page 13, paragraph 0059).
Boyne et al. do not explicitly teach the aptamer and effector stem loop are linked by an alternatively shared stem arm comprising sequence that is complementary to the unshared arm of the aptamer stem and to the unshared arm of the effector stem loop. Boyne et al. however teach further stability through both stem length and complementary sequences. The shared arm of the aptamer (sensor) and effector stem would have complementarity to the unshared arm of the aptamer in order to form the stem loop structure of the hairpin. Furthermore, the additional stem of the effector would have complementarity to the shared arm well, because it comprises sequence from the aptamer stem. Therefore the suggestions of Boyne et al. would have made it obvious to engineer a riboswitch where the aptamer and the effector form a stable structure and further optimize the linker between aptamer and effector. The optimization of the linker would provide a more stable structure by including a linker with the alternatively shared stem arm, which would form into a stable structure based on sequence complementarity.
Regarding claim 2, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. teach the aptamer binds a small molecule ligand (page 1, paragraph 0002).
Regarding claim 3, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. do not teach the portion of the alternatively shared stem arm that is complementary to sequence in the aptamer stem and to sequence in the effector stem loop is 4 to 8 nucleotides, 5 to 7 nucleotides, 5 nucleotides, or 6 nucleotides. Boyne et al. teaches the aptamer directly linked to the effector to form a hairpin stem (page 13, paragraph 0056) and further the length must be optimal for stable stem structure (page 35, paragraph 0153). Therefore, it would have been obvious to one of ordinary skill in the art to perform routine experimentation to optimize the length of the shared sequence between aptamer and effector for a stable structure to be formed.
Regarding claim 4, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. do not specifically teach wherein the aptamer stem is 6 to 12 base pairs, 7 to 10 base pairs, 8 base pairs, or 9 base pairs. Boyne et al. teach that aptamer stem can be optimized based on the ligand used and desired expression level of the gene (pages 13-14, paragraph 0059). Boyne et al. teach the aptamer will typically be between about 15 and about 200 nucleotides in length (page 14, paragraph 0062).Therefore one of ordinary skill in the art would perform routine experimentation to optimize the length of the aptamer stem to achieve a desired sensitivity to the ligand and desired expression level for the gene of interest.
Regarding claim 5, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. teach the effector stem loop is between about 7 base pairs to about 20 base pairs (page 13, paragraph 0059), which reads on the effector stem loop is 4 to 24 base pairs, 5 to 20 base pairs, 9 to 14 base pairs, 9 base pairs, 10 base pairs, 11 base pairs or 12 base pairs.
Regarding claim 6, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. teach the effector stem includes the 5’ splice site of the 3’ intron (page 2, paragraph 0001), which reads on the effector stem loop is positioned is positioned 3’ of the aptamer. Boyne et al. teach the aptamer is directly linked to the effector which forms a hairpin stem (page 13, paragraph 0056). Boyne et al. further teach the length must be optimal for stable stem structure (page 35, paragraph 0153). Therefore, it would have been obvious to one of ordinary skill in the art to perform routine experimentation to optimize the length of the shared sequence between aptamer and effector for a stable structure to be formed.
Regarding claim 7, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. teach the polyadenylation signal is a SV40 polyadenylation signal but does not explicitly teach the signal is AATAAA. However, an SV40 polyadenylation signal is AATAAA as evidenced by Li et al.
Regarding claim 8, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. teach the effector stem loop is positioned 5' of the aptamer (figure 4c). Boyne et al. teach the effector region comprises a stem sequence, in addition to the 5' ss sequence of the 3' intron and its complementary sequence. Boyne et al. teach the additional stem sequence comprises a sequence from the aptamer stem. Boyne et al. further teach length and sequence of the stem portion can be modified using known techniques in order to identify stems that allow acceptable background expression of the target gene when no ligand is present and acceptable expression levels of the target gene when the ligand is present (pages 13-14, paragraph 0059).
Regarding claim 9, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 8. Boyne et al. teach the SV40 polyadenylation signal is downstream of the riboswitch element (page 45, paragraph 00212); therefore, the polyadenylation signal is a downstream element.
Regarding claim 13, Boyne et al. teach a method of modulating the expression of a target gene comprising (a) inserting the polynucleotide cassette as described above in regard to claim 1 into the target gene, (b) introducing the target gene comprising the polynucleotide cassette into a cell, and (c) exposing the cell to a small molecule ligand that specifically binds the aptamer in an amount effective to induce expression of the target gene (page, paragraph 0005).
Regarding claim 14, Boyne et al. make obvious a method of modulating the expression of a target gene as described above in regard to claim 13. Boyne et al. further teach the ligand is a small molecule ligand (page 13, paragraph 0054).
Regarding claim 15, Boyne et al. make obvious a method of modulating the expression of a target gene as described above in regard to claim 13. Boyne et al. teach the effector stem includes the 5’ splice site of the 3’ intron (page 2, paragraph 0001), which reads on the effector stem loop is positioned is positioned 3’ of the aptamer. Boyne et al. teaches the aptamer directly linked to the effector to form a hairpin stem (page 13, paragraph 0056). Boyne et al. further teach the length must be optimal for stable stem structure (page 35, paragraph 0153). Therefore, it would have been obvious to one of ordinary skill in the art to perform routine experimentation to optimize the length of the shared sequence between aptamer and effector for a stable structure to be formed.
Regarding claim 16, Boyne et al. make obvious the method as described above in regard to claim 15. Boyne et al. teach the polyadenylation signal is a SV40 polyadenylation signal but does not explicitly teach the signal is AATAAA. However, an SV40 polyadenylation signal is AATAAA as evidenced by Li et al.
Regarding claim 17, Boyne et al. make obvious a method of modulating the expression of a target gene as described above in regard to claim 13. Boyne et al. teach the effector stem loop is positioned 5' of the aptamer (figure 4c). Boyne et al. teach the stem portion of the effector region comprises stem sequence in addition to the 5' ss sequence of the 3' intron and its complementary sequence. Boyne et al. teach the additional stem sequence comprises sequence from the aptamer stem. Boyne et al. further teach the length and sequence of the stem portion can be modified using known techniques in order to identify stems that allow acceptable background expression of the target gene when no ligand is present and acceptable expression levels of the target gene when the ligand is present (pages 13-14, paragraph 0059).
Regarding claim 18, Boyne et al. make obvious the method as described above in regard to claim 17. Boyne et al. teach the SV40 polyadenylation signal is downstream of the riboswitch element (page 45, paragraph 00212); therefore, the polyadenylation signal is a downstream element.
Regarding claim 23, Boyne et al. make obvious a method of modulating the expression of a target gene as described above in regard to claim 13. Boyne et al. teach the target gene comprising the polynucleotide cassette is incorporated in a vector for the expression of the target gene (page 3, paragraph 0008).
Regarding claim 24, Boyne et al. make obvious a method of modulating the expression of a target gene as described above in regard to claim 13. Boyne et al. teach a polynucleotide gene regulation cassette placed in the target gene for modulation of the target gene expression. Boyne et al. further teach modulation of the target gene by aptamer-mediated regulation of alternative splicing (page 2 paragraph 0001).
Regarding claim 25, Boyne et al. make obvious a method of modulating the expression of a target gene as described above in regard to claim 13. Boyne et al. further teach the vector is a viral vector (page 3, paragraph 0008).
Regarding claim 26, Boyne et al. make obvious the method described above in regard to claim 25. Boyne et al. teach the viral vector is the viral vector is selected from the group consisting of adenoviral vectors, adeno-associated virus vectors, and lentiviral vectors (page 3, paragraph 0008).
Regarding claim 27, Boyne et al. teach a vector comprising a target gene (page 3, paragraph 0008). Boyne et al. make obvious the polynucleotide cassette as described above in regard to claim 1.
Regarding claim 28, Boyne et al. make obvious the vector as described above in regard to claim 27. Boyne et al. further teach the vector is a viral vector (page 3, paragraph 0008).
Regarding claim 29, Boyne et al. make obvious the vector as described above in regard to claim 28. Boyne et al. teach the vector is the viral vector is selected from the group consisting of adenoviral vectors, adeno-associated virus vectors, and lentiviral vectors (page 3, paragraph 0008).
Regarding claim 30, Boyne et al. make obvious the vector as described above in regard to claim 27. Boyne et al. teach a polynucleotide gene regulation cassette that is placed in the target gene to modulate target gene expression. Boyne et al. teach modulation of target gene expression by aptamer-mediated regulation of alternative splicing (page 2 paragraph 0001).
Regarding claim 31, Boyne et al. make obvious the polynucleotide cassette as described above in regard to claim 8. Boyne et al. teach the polyadenylation signal is an SV40 polyadenylation signal, but does not explicitly teach the signal is AATAAA. However, an SV40 polyadenylation signal is AATAAA as evidenced by Li et al.
Regarding claim 32, Boyne et al. make obvious the polynucleotide cassette as described above in regard to claim 8. Boyne et al. teach the SV40 polyadenylation signal is downstream of the riboswitch element (page 45, paragraph 00212); therefore, the polyadenylation signal is a downstream element.
Regarding claim 33, Boyne et al. make obvious the method as described above in regard to claim 17. Boyne et al. teach the polyadenylation signal is a SV40 polyadenylation signal but does not explicitly teach the signal is AATAAA. An SV40 polyadenylation signal is AATAAA as evidenced by Li et al.
Regarding claim 34, Boyne et al. make obvious the method as described above in regard to claim 15. Boyne et al. teach the SV40 polyadenylation signal is downstream of the riboswitch element (page 45, paragraph 00212); therefore, the polyadenylation signal is a downstream element.
Claims 10-12 and 19-22 are rejected under 35 U.S.C. 103 as being unpatentable over Boyne et al. (WO 2016/126747 Al) as evidenced by Li et al. (2012) as applied to claims 1 and 13 above, and further in view of Sharma et al. (Journal of the American Chemical Society, 2008).
Boyne et al. make obvious claims 1 and 13 as set forth above.
Regarding claim 10, Boyne et al. make obvious the polynucleotide cassette described above in regard to claim 1. Boyne et al. teach the polyadenylation signal is a SV40 polyadenylation signal but does not explicitly teach the signal is AATAAA. However, an SV40 polyadenylation signal is AATAAA as evidenced by Li et al.
Boyne et al. do not teach the cassette comprises two riboswitches.
Sharma et al. teach engineering complex riboswitches capable of sensing and responding to two small molecules (page 16310, abstract). Sharma et al. teach two aptamers that recognize two small molecules and the riboswitches function as logic gates supporting the versatility of RNA-based gene regulation. Sharma et al. teach the strategy advances the ability to harness the versatile capabilities of RNA to program complex behavior (page 16310, abstract).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to have combined the teachings of Boyne et al. for a polynucleotide cassette for the regulation of the expression of a target gene comprising a riboswitch with the teachings of Sharma et al. for complex riboswitches capable of sensing and responding to two small molecules. Sharma et al. provide motivation by teaching that ability to harness the versatile capabilities of RNA to program complex behavior. One of skill in the art would have had a reasonable expectation of success at combining Boyne et al. and Sharma et al. because both teach methods of expression regulation via riboswitches. Further both the effector stem loops would comprise all or part of the downstream element a polyadenylation signal
Regarding claim 11, Boyne et al. and Sharma et al. make obvious the polynucleotide cassette described above in regard to claim 10. Boyne et al. teach regulatory cassettes with different intron and exon sequences may be used in a single target gene, and these may contain the same ligand responsive aptamers (page 41, paragraph 00187). Therefore, Boyne et al. and Sharma et al. make obvious the two riboswitches each comprise an aptamer that binds the same ligand.
Regarding claim 12, Boyne et al. and Sharma et al. make obvious the polynucleotide cassette described above in regard to claim 10. Sharma et al. teach the riboswitch includes two distinct aptamer ligands (page 16311, right column).
Regarding claim 19, Boyne et al. make obvious the method of claim 13. Boyne et al. teach the polyadenylation signal is a SV40 polyadenylation signal but does not explicitly teach the signal is AATAAA. However, an SV40 polyadenylation signal is AATAAA as evidenced by Li et al.
Sharma et al. teach engineering complex riboswitches capable of sensing and responding to two small molecules (page 16310, abstract). Sharma et al. teach two aptamers that recognize theophylline and thiamine pyrophosphate were embedded in tandem in the 5′ UTR of bacterial mRNA, and riboswitches that function as logic gates were isolated by dual genetic selection (page 16310, abstract). Sharma et al. teach two aptamers that recognize two small molecules and the riboswitches function as logic gates supporting the versatility of RNA-based gene regulation. Sharma et al. teach the strategy advances the ability to harness the versatile capacities of RNA to program complex behavior (page 16310, abstract).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to have combined the teachings of Boyne et al. for a polynucleotide cassette for the regulation of the expression of a target gene comprising a riboswitch with the teachings of Sharma et al. for complex riboswitches capable of sensing and responding to two small molecules. Sharma et al. provide motivation by teaching the ability to harness the versatile capacities of RNA to program complex behavior. One of skill in the art would have had a reasonable expectation of success at combining Boyne et al. and Sharma et al. because both teach methods of expression regulation via riboswitches. Further both the effector stem loops would comprise all or part of the downstream element a polyadenylation signal
Regarding claim 20, Boyne et al. and Sharma et al. make obvious the method as described above in regards to claim 19. Boyne et al. teach regulatory cassettes with different intron and exon sequences may be used in a single target gene, and these may contain the same ligand responsive aptamers (page 41, paragraph 00187). Therefore, Boyne et al. and Sharma et al. make obvious the two riboswitches each comprise an aptamer that binds the same ligand.
Regarding claim 21, Boyne et al. and Sharma et al. make obvious the method as described above in regard to claim 19. Sharma et al. teach the riboswitch includes two distinct aptamer ligands (page 16311, right column).
Regarding claim 22, Boyne et al. and Sharma et al. make obvious the method as described above in regard to claim 19. Boyne et al. teach regulatory cassettes with different intron and exon sequences may be used in a single target gene, and these may contain the same ligand responsive aptamers (page 41, paragraph 00187). Therefore, Boyne et al. and Sharma et al. make obvious the two riboswitches of the polynucleotide cassettes comprise the same aptamer.
Conclusion
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/C.L.M./Examiner, Art Unit 1638
/Anna Skibinsky/
Primary Examiner, AU 1635