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 .
Election/Restrictions
Applicant's election with traverse of the invention of Group 1 (methods of ligating a first and second fragment), and the particular species that are: T4 RNA Ligase II; base modification, 2’OMe; and a protease, in the reply filed on 10/15/2025 is acknowledged.
Please note that in light of the Examiner’s analysis of the elected subject matter, the species election requirement between the elected species “protease” and the species “crowding agent” is withdrawn.
The traversal is on the ground(s) that the common technical feature between groups 1 and 2 of the requirement of 04/18/2025 is a special technical feature because the feature is not provided by the prior art cited in the requirement. This is not found persuasive because the rejections set forth in the Instant Office Action provide evidence that any common technical feature is not a special technical feature.
The requirement is still deemed proper and is therefore made FINAL.
Claims 40, 50, 81 and 82 withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention (i.e.: requiring three nucleic acids molecules to be ligated to for a single nucleic acid molecule), there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 10/15/2025.
Specification
The disclosure is objected to because of the following informalities:
The description of Fig 4 on page 13 of the Specification as filed provides:
FIG. 4 is an illustration showing locations for segmenting an exemplary gRNA molecule (SEQ ID NO: 16) into RNA fragments (RNA fragment 1,RNA fragment 2, and RNA fragment 3 having nucleotide sequences set forth in SEQ ID NOs: 56, 3, and 4 respectively).
But the sequence depicted in the figure is not SEQ ID NO: 16 nor is a portion of the depicted sequence SEQ ID NO: 56, because the depicted sequence only has 20 N positions at the 5’ end, whereas each of SEQ ID NO: 16 and 56 has 30 N positions at the 5’ end. The specification may be made more clear in this regard if amended to recite:
FIG. 4 is an illustration showing locations for segmenting an exemplary gRNA molecule (positions 11-110 of SEQ ID NO: 16) into RNA fragments (RNA fragment 1,RNA fragment 2, and RNA fragment 3 having nucleotide sequences set forth in positions 11-43 of SEQ ID NO[[s]]: 56, and SEQ ID NOs: 3, and 4 respectively).
Appropriate correction is required.
Claim Rejections - 35 USC § 103
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.
Claim(s) 1, 5, 6, 13, 16, 29, 30, 31, 43, 76, 77 and 95 is/are rejected under 35 U.S.C. 103 as being unpatentable over Singer et al (US PG Pub 20170268035 A1) in view of Akiyama et al (2009).
Relevant to the limitations of claim 1, Singer et al exemplifies a method of synthesizing a sgRNA (claim 43) including ligations of a first RNA fragment and a second RNA fragment, where a fragment includes a portion that can bind to an RNA-guided endonuclease, in the presence of a DNA splint oligonucleotide (claim 6) (e.g.: para 00119-0120; Table 1).
Relevant to claim 13, the ligation site between SEQ ID NOs: 9 and 10 of Singer et al is in a helix portion of a stem loo structure.
Relevant to claim 16, Singer et al teaches that a plurality of different sgRNA complexes (with different sgRNA targeting different sequences) can be used for multicolor imaging (e.g.: para 0133-0134).
Relevant to claim 76 and 77, Singer et al teaches that the ligated sgRNA molecule can bind to Cas9 (e.g.: para0019; para 0129-130). It is noted that the reference exemplifies the binding of the sgRNA to a deactivated Cas9 (dCas9), while the dCas9 does not have endonuclease activity, the teaching in the reference is evidence that the prior art sgRNA is can bind to Cas9, as required by the claims.
Singer et al does not specify the end structures of the RNA fragments, or an RNA ligase, as recited in claim 1. However, such elements in the ligation of RNA fragments were known in the prior art and are taught by Akiyama et al.
Relevant to claim 1, Akiyama teaches the ligation of an RNA with a 5’-monophosphate to an RNA fragment having a 3’-hydroxyl group in the presence of a DNA splint using T4 RNA ligase II (claim 5) (e.g.: p.40 – RNA Ligation Methods; Fig. 2.5).
Relevant to claims 29-31, Akiyama et al teaches and annealing step (claim 95) comprising hybridizing the RNA fragments and splint oligonucleotide in a solution with about equal concentrations of the nucleic acids (e.g.: p.43 - Annealing of DNA Splints to precursor RNA fragments), and teaches ligation at 30oC for 2 hours (e.g.: p.43 - Ligation reaction).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have performed sgRNA synthesis by splint ligation of Singer et al using the methodological steps and particular reagents of Akiyama et al. The skilled artisan would have been motivated to use the methods of Akiyama et al based on the expressed teachings of Akiyama et al that the use of RNA ligation for covalently joining multiple RNA fragments allows for the production of longer RNAs. The skilled artisan would have a reasonable expectation of success because Akiyama et al provides a detailed protocol for the ligation of RNA fragments using T4 RNA ligase II. With regard to the rejection of claim 16, where Singer et al teaches the use of different sgRNAs to target different genomic loci, it would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to make each of the different sgRNAs using the same methods rendered obvious by Singer et al in view of Akiyama et al. Making a plurality of different sgRNAs would thus provide the ligation of additional different RNA fragments among the different sgRNAs.
Claim(s) 8 is/are rejected under 35 U.S.C. 103 as being unpatentable over Singer et al (US PG Pub 20170268035 A1) in view of Akiyama et al (2009) as applied to claims 1, 5, 6, 13, 16, 29, 30, 31, 43, 76, 77 and 95 above, and further in view of Badenhorst et al (WO 2019/159958).
Singer et al in view of Akiyama et al renders obvious methods of synthesizing a sgRNA by ligation of RNA fragments using a splint oligonucleotide and an RNA ligase.
Singer et al in view of Akiyama et al does not provide for a splint oligonucleotide attached to a solid support, as recited in claim 8.
However, the use of oligonucleotides bound to solid supports was known in the prior art and is taught by Badenhorst et al.
Badenhorst et al teaches that products of splint ligation may be enriched by capture via target-specific probes bound to solid support (e.g.: p.2).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have performed the splint ligation methods rendered obvious by Singer et al in view of Akiyama et al using a splint oligonucleotide that is bound to a solid support. The skilled artisan would have been motivated to provide a splint oligonucleotide that is bound to a solid support based on the expressed teachings of Badenhorst et al that a solid-support-bound oligonucleotide may function to enrich target nucleic acids. The skilled artisan would have a reasonable expectation of success in using a splint oligonucleotide that is bound to a solid support based on the expressed teachings of Singer et al and Akiyama et al which exemplify splint probes that are complementary to the ligated product, and thus would be suitable for enrichment of the target via hybridization.
Claim(s) 24 and 25 is/are rejected under 35 U.S.C. 103 as being unpatentable over Singer et al (US PG Pub 20170268035 A1) in view of Akiyama et al (2009) as applied to claims 1, 5, 6, 13, 16, 29, 30, 31, 43, 76, 77 and 95 above, and further in view of Smith et al (US PG Pub 2019/0316121).
Singer et al in view of Akiyama et al renders obvious methods of synthesizing a sgRNA by ligation of RNA fragments using a splint oligonucleotide and an RNA ligase.
Singer et al in view of Akiyama et al does not provide for a base modification, in particular 2’-O-methoxy (2’OMe, as consonant with the election) in the sgRNA.
However, the use of 2’OMe modified bases in sgRNAs was known in the prior art and is taught by Smith et al.
Smith et al teaches that sgRNAs may contain modified bases, including 2′-O-methyl (2′-O-Me) (e.g.: para 0006; Table 4).
Note that “2'-methoxy” and “2'-O-methoxy” (or 2'-MOE) refer to the same common chemical modification in nucleic acids, where a methoxy group (-OCH3) is attached to the 2'-hydroxyl 2’-OH) of the ribose sugar.
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have performed the splint ligation methods rendered obvious by Singer et al in view of Akiyama et al using a sgRNA fragments that include 2’OMe modified bases. The skilled artisan would have been motivated to provide sgRNA fragments that include 2’OMe modified bases based on the expressed teachings of Smith et al modified bases in the sgRNA may improve stability of sgRNA (e.g.: paras: 0004; 0005; 0151). The skilled artisan would have a reasonable expectation of success bases based on the expressed teachings of Smith et al which exemplifies the production and use of such modified sgRNAs.
Claim(s) 34 is/are rejected under 35 U.S.C. 103 as being unpatentable over Singer et al (US PG Pub 20170268035 A1) in view of Akiyama et al (2009) as applied to claims 1, 5, 6, 13, 16, 29, 30, 31, 43, 76, 77 and 95 above, and further in view of Moore et al (US PG Pub 20150099671).
Singer et al in view of Akiyama et al renders obvious methods of synthesizing a sgRNA by ligation of RNA fragments using a splint oligonucleotide and an RNA ligase.
Singer et al in view of Akiyama et al does not provide for a ligation reaction that comprises using a crowding agent.
However, the use of crowding agents in ligation reactions was known in the prior art and is taught by Moore et al.
Moore et al teaches that crowding agents including PEG8000 are added to nucleic acid ligation reaction (e.g.: para 0084).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have performed the splint ligation methods rendered obvious by Singer et al in view of Akiyama et al using a crowding agent. The skilled artisan would have been motivated to provide a crowding agent based on the expressed teachings of Moore et al that molecular crowding agents can sometimes increase enzyme reaction efficiency. The skilled artisan would have had a reasonable expectation of success based on the expressed exemplification of Moore et al that including PEG8000 at 25% resulted in near improved ligation of nucleic acids.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 5-6, 8, 13, 16, 24-25, 29-31, 34, 43, 76-77 and 95 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6, 23-31, 34, 40, 61, 85, 86, and 129 of copending Application No. 17/934,799 (reference application).
The instantly rejected claims are also provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6, 23-31, 34, 40, 61, 85, 86, and 129 of copending Application No. 17/934,799 (reference application) in view of Singer et al (US PG Pub 20170268035 A1), Akiyama et al (2009), Badenhorst et al (WO 2019/159958), Smith et al (US PG Pub 2019/0316121), and Moore et al (US PG Pub 20150099671) where the teachings of the additional art is applied to the rejected claims as previously set forth in this Office Action.
Although the claims at issue are not identical, they are not patentably distinct from each other because the conflicting claims are directed to the synthesizing the same nucleic acid product (i.e.: a guide RNA (gRNA)) using a splint ligation method and recite the same enzyme (i.e.: RNA ligase, see conflicting claim 28).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is allowed.
The relevant art made of record and not relied upon is considered pertinent to applicant's disclosure. The output from a folding of the RNA sequence of positions 21-36 of SEQ ID NO: 9 and positions 1-24 of SEQ ID NO: 10 from Singer et al indicates the location of the ligation site as site in a helix portion of a stem-loop structure in the synthesized sgRNA.
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683