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 .
This Office Action is in reply to Applicants’ correspondence of 06/23/2026.
Applicants’ remarks and amendments have been fully and carefully considered but are not found to be sufficient to put the application in condition for allowance. No new grounds of rejection are presented in this Office Action. Any rejections or objections not reiterated herein have been withdrawn in light of the amendments to the claims or as discussed in this Office Action.
This Action is made FINAL.
Please Note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Election/Restrictions
In the reply filed on 10/15/2025 Applicants elected, with traverse, 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, 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matter, the species election requirement between the elected species “protease” and the species “crowding agent” was withdrawn.
The requirement was deemed proper and made FINAL as set forth on page 2 of the Office Action of 01/23/2026
Claims 40, 50, 81 and 82 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b), as set forth on pages 2-3 of the Office Action of 01/23/2026.
Withdrawn Objection to the Specification
The objection to the disclosure, as set forth on page 3 of the Office Action of 01/23/2026, is withdrawn in light of the amendments to the specification provided with the reply of 06/23/2026, which are entered.
Maintained Claim Rejections – 35 USC § 103
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.
Response to Remarks
Applicants have traversed the rejection of claims under 35 USC 103 as obvious in view of the cited prior art. Applicants’ arguments (p.11-14 of the Remarks of 06/23/2026) have been fully considered but are not persuasive to withdraw the rejection.
Applicants initially address the teachings of Singer, pointing out that Singer does not provide detailed information on the ligation process. This argument is not persuasive because the rejection includes the teachings of Akiyama et al which clearly provides detailed information on the process of ligating structured RNAs using a splint oligo.
Applicants next argue that the 5’ and 3’ RNA arms of Singer hybridize to the splint of Singer with complementarity at the junction of the arms without the DNA splint showings a single-stranded portion at the junction of the two. This argument is not persuasive because the rejection includes the teachings of Akiyama et al which clearly provides that T4 RNA ligase 2 prefers a double stranded composition for ligation (e.g.: Figure 2.5).
Applicants next argue that Singer teaches generation of a fluorescently labeled sgRNA (whereas unlabeled sgRNAs are synthesized in vitro from template DNA by using T7 RNA polymerase) and conclude that Singer teaches away from using splint-mediated ligation for synthesizing unlabeled sgRNAs. But such a conclusion (i.e.: that Singer teaches away from splint-mediated ligation for synthesizing unlabeled sgRNAs) is not accurate. Initially it is noted that synthesis of a labeled sgRNA is within the scope of the methods of the rejected claims. Furthermore, as noted in MPEP 2145(X)(D)(I):
… "the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004). See also UCB, Inc. v. Actavis Labs, UT, Inc., 65 F.4th 679, 692, 2023 USPQ2d 448 (Fed. Cir. 2023) ("a reference does not teach away if it merely expresses a general preference for an alternative invention but does not criticize, discredit or otherwise discourage investigation into the invention claimed.") (
Finally in this regard it is noted that the rejection includes the teachings of Akiyama et al which clearly provides labeled fragments of structured RNAs that are ligated with T4 RNA ligase 2 using a splint oligo (Fig. 2.5).
Applicants’ arguments next address alleged shortcomings of the teachings of Akiyama. Applicants argue (p.12 of the Remarks) that the reference teaches the unwanted side products that may be formed using T4 RNA ligase. This argument is not persuasive because it does not consider the full teachings of the cited reference which include that T4 RNA ligase 2 prefers double-stranded nucleic acid (thus decreasing the production of unwanted side products) and that T4 RNA ligase 2 is highly active (Fig 2.5). The argument ignores the plain teachings of Akiyama “we typically use T4
RNA ligase 2 for our splinted RNA ligation reactions” (p.42). Applicants selectively point to the teaching of Akiyama that “for certain joining reactions we have found it necessary to use the less efficient T4 DNA ligase enzyme to suppress unwanted reaction products”, but there is no evidence or indication that the type of ligation taught by Singer (the teachings of which are combined with Akiyama in the instant rejection) would be such a “certain joining reaction”. Furthermore Applicants’ arguments ignore the beneficial nature of the cost of using T4 RNA ligase 2 that is explicitly provided in Akiyama: when using T4 RNA ligase 2 one can use far less enzyme to achieve comparable levels of RNA ligation to that of T4 DNA ligase-catalyzed reactions, making this approach significantly more cost-effective.
Applicants’ traversals of the subsequent rejections are based on the same rationales, and are thus similarly not persuasive to withdraw the rejections reiterated below.
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.
Maintained Rejection - 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.
Response to Remarks
Applicants have acknowledged the rejection on p.15 of the Remarks of 06/23/2026.
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.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHEN THOMAS KAPUSHOC whose telephone number is (571)272-3312. The examiner can normally be reached M-F, 8am-5pm.
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683
Prosecution Insights