DETAILED ACTION
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Applicant’s Request for Continued Examination, Amendment and Arguments/Remarks received on 09 July 2026 have been entered.
Claims 1, 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, 469, and 471-474 were previously pending in the application. No claims have been cancelled, and no new claims have been added by Applicant. Claims 1, 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, 469, and 471-474 are currently pending in the application. Claims 1, 97, 452, 453, 454, 463, 464, and 472 are independent claims.
The election of the following species remains in effect in the instant application:
SEQ ID NOs: 302 and 3530 expanded to include the subject matter of claim 458.
Claims 1, 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, 469, and 471-474 are currently pending and under examination in the instant application. An action on the merits follows.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Priority
The present application is a CON of 35 International Application No. PCT/US2019/036160, filed 07 June 2019, which claims priority to U.S. Provisional Application No. 62/682,838, filed 08 June 2018, and U.S. Provisional Application No. 62/682,820, filed 08 June 2018.
Thus, the earliest possible priority for the instant application is 08 June 2018.
Information Disclosure Statement
The information disclosure statement filed 09 July 2026 has been considered by the Examiner.
Claim Rejections - 35 USC § 112(b)
The rejection of amended claim 469 under 35 U.S.C. 112(b) as failing to particularly point out and distinctly claim the subject matter which the inventor(s) regards as the invention for reciting “the mRNA” is withdrawn.
Amended, previously presented, and original claims 1, 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, 469, and 471-473 are newly rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claims 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, 469, 471, and 473 are included in this rejection due to their dependence on and/or encompassing of independent claim 1 and/or 472.
Independent claim 1 recites, “the conserved portion comprises… vii) a hairpin region, wherein the hairpin region comprises… (a) a hairpin 1 region being nucleotides H1-1 to H1-12, (b) a nucleotide, and (c) a hairpin 2 region being nucleotides H2-1 to H2-15, and wherein (1) the hairpin 1 region lacks 5-10 of the nucleotides within the hairpin 1 region or within the hairpin 1 region and the nucleotide between the hairpin 1 region and the hairpin 2 region” in lines 2-3 and 10-17, which is indefinite because it is unclear how the conserved portion can both comprise a hairpin region comprising (a) a hairpin 1 region being nucleotides H1-1 to H1-12, (b) a nucleotide, and (c) a hairpin 2 region being nucleotides H2-1 to H2-15 and also lack 5-10 nucleotides of the regions of (a) or (a) + (b). For example, it is unclear whether the nucleotides recited in (a) and (b) include the 5-10 which are lacking or whether the nucleotides recited in (a) and (b) are meant to already lack the 5-10 nucleotides. If the former, then it is unclear what the 5-10 nucleotides are lacking relative to and how the number of lacking nucleotides can be variable for a fixed number of nucleotides present. If the former, then reciting that the sgRNA comprises the nucleotides of (a) and (b) but also lacks some of the nucleotides of (a) and (b) are conflicting limitations within the claim.
Similarly, independent claim 472 recites, “the conserved portion comprises… vii) a hairpin region, wherein the hairpin region comprises… (a) a hairpin 1 region being nucleotides H1-1 to H1-12, (b) a nucleotide, and (c) a hairpin 2 region being nucleotides H2-1 to H2-15, and wherein (1) the hairpin 1 region lacks 5-10 of the nucleotides within the hairpin 1 region” in lines 2-3 and 10-15, which has the same issues of indefiniteness as discussed above for independent claim 1.
As such, the metes and bounds of the claim cannot be determined.
Claim Rejections - 35 USC § 103
The rejection of amended, previously presented, and original claims 1, 5, 13-14, 16, 25, 437, 443, 452-458, 463-466, and 471-474 under 35 U.S.C. 103 as being unpatentable over May et al. [US20150376586A1, IDS, published 31 December 2015, cited in a prior office action]; in view of Yin et al. [2017, Nature Biotechnology, 35(12), 1179-1187, IDS]; Wang et al. [2017, Chemical Reviews, Vol. 117, 9874-9906, cited in a prior office action]; and Mir et al. [2018, BioRxiv [preprint], deposited 28 March 2018, cited in a prior action]; is maintained. Applicant's amendments to the claims and arguments have been fully considered but have not been found persuasive in overcoming the rejection for reasons of record as discussed in detail below.
Applicant amended claim 453 for clarity and did not amend any other claims. As such, Applicant did not alter the scope of the claims sufficiently to overcome a finding of obviousness under 35 U.S.C. 103 over May, Yin, Wang, and Mir.
Applicant argues that none of May, Yin, Wang, and Mir, along or in combination, provide any basis for an ordinarily skilled artisan to select the upper stem region of a sgRNA which “lacks 5-10 of the nucleotides within the hairpin 1 region or within the hairpin 1 region and the nucleotide between the hairpin 1 region and the hairpin 2 region” and modify it such that “at least 10 nucleotides of the upper stem region comprise 2’-O-methyl (2’-O-Me) modifications”; nor would any of the cited references have provided any reason or motivation for the ordinarily skilled artisan to select and incorporate the claimed specific chemical modification in the specific claimed region into guide RNAs with the specific claimed structure; in that:
1) Yin does not motivate modifying the upper stem loop and teaches away from altering the hairpin in that the sgRNAs of Yin are not limited to 2’-OMe modifications within the stem loop region and Yin does not teach that chemical modifications such as 2’-O-Me improve therapeutic efficacy by reducing susceptibility to nuclease degradation irrespective of the underlying gRNA sequence;
2) the sgRNAs of Yin also include extensive 2’-O-Me modification of the hairpin 1 region, but the instant claims recite that the hairpin 1 region lacks 5-10 nucleotides;
3) Yin cautions against departure from the specific sgRNAs for which Yin provides experimental results by reciting “Chemical modifications can interfere with the biological function of therapeutic RNAs” [pg 1179 col 2 ¶ 2] and that “judicious chemical modification of RNAs can improve therapeutic efficacy” [abstract], wherein different RNA sequences have different patterns of sensitivity to chemical modification in that certain chemical modification can interfere with the activity of the siRNA-Argonaut complex and ASOs show a different pattern of sensitivity to chemical modifications [pg 1179 col 2 ¶ 2-pg 11870 col 3 ¶ 1;
4) Ryan [WO2016/089433A1] shows that changes in the positions of modifications (such as 2’-O-Me) can result in a complete loss of sgRNA activity; and
5) it was not predictable whether Yin’s teachings could extend to sgRNAs with an altered hairpin 1 region because Yin cautions that altering the secondary structure of the hairpin 1 region is undesirable in that “incorporating 2’F-modified RNA into these two loops significantly decreased the activity of sgRNA in cells… [i]t is possible that the 2’F modification within loops influences their secondary structure” [pg 1180 col 4 ¶ 2], such that Yin’s teaching that changes in secondary structure can alter the activity of sgRNAs would lead an ordinarily skilled artisan to understand that different RNA sequences have different patterns of sensitivity to chemical modifications, further leading to an expectation that the absence of residues within the hairpin 1 region would influence secondary structure, and that such a change in secondary structure could alter the pattern of sensitivity to chemical modification, thereby dissuading the ordinarily skilled artisan from combining the 2’-O-Me modifications of Yin with sgRNA structures of May.
However, this is not agreed.
In response to Applicant’s arguments against the references individually, it is noted that the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Further, the Examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In addition, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Specifically, regarding Applicant’s argument 1), note that independent claim 1 as written does not require any hairpin 1 nucleotides remaining to be unmodified.
Yin was cited for teaching the motivation to incorporate 2’-O-Me modifications in the upper stem loop nucleotides at all of the upper stem loop nucleotides to improve cleavage efficiency and to increase RNA resistance to degradation [abstract, column 2 ¶ 2, column 9 ¶ 3- column 10 ¶ 1, Figure 1, 3-4].
Specifically, Yin was cited for teaching testing modifications within the invariable region of the sgRNAs, such that sgRNAs comprising 2’-OMe modifications at either eight or every nucleotide of the stem loop (e.g., 2’OMe_loops, SG-2’OMe, and SG-2’OMe-PS) have the highest efficiency of all tested modification variants and also have higher efficiency than the unmodified sgRNA [Figure 1]. Yin further teaches the combination of modifications within the variable (guide) sequence in combination with modifications in the invariable region, in which the sgRNA comprising 2’-OMe modifications at every nucleotide of the upper stem region (e.g., e-sgRNA) outperformed both the native sgRNA and the 5’&3’ end labeled sgRNA in cleavage efficiency (e.g., on-target indel formation) in both human cells and in mice [Figures 3-4]. Yin also teaches that chemical modifications of RNAs, including 2’-O-Me modification, can improve therapeutic efficacy by reducing susceptibility to nuclease degradation and that the modification of e-sgRNA facilitate function in part by increasing RNA resistance to degradation [abstract, column 2 ¶ 2, column 9 ¶ 3- column 10 ¶ 1]. Therefore, an ordinarily skilled artisan at the time of filing the instant application would have been motivated to incorporate 2’-O-Me modifications in the upper stem loop nucleotides, including at least 8 and up to all of the upper stem loop nucleotides, to improve cleavage efficiency and to increase RNA resistance to degradation.
Regarding Applicant’s argument 2), as discussed in the prior action, May was cited for teaching a sgRNA lacking 5-10 nucleotides in the hairpin 1 region (i.e., SEQ ID NO: 1467 which has 100% sequence identity to elected instant SEQ ID NO: 307). As such, any teachings of Yin that modifications within those deleted nucleotides may alter the secondary structure of the sgRNA cannot apply to a sequence which does not comprise those nucleotides. Additionally, alterations to secondary structure resulting from disrupting hydrogen bonding by replacing the 2’-OH with a 2’F are not equivalent to changes in secondary structure resulting from a deletion of a nucleotides. May was cited for teaching elimination of nucleotides from the hairpin 1 region. May further teaches wherein deletion of 8-10 nucleotides of hairpin 1 increases cleavage activity [Figure 16]. Thus, teaching away from specifically modifying hairpin 1 nucleotides with 2’F modifications is not relevant to the obviousness rejection over May in view of Yin, Wang, and Mir.
Regarding Applicant’s argument 3), note that the teachings of certain modifications interfering with the activity of siRNA-Argonaut complex or anti-sense oligonucleotides (ASOs) is not relevant in light of teachings of the effects of modifications on sgRNAs invariable regions, in that the sgRNAs of May and Yin are interacting with the same Cas9 protein whereas siRNAs and ASOs have different RNA-protein and RNA-RNA or RNA-DNA interactions required for their activity compared to those required for sgRNAs. However, the teachings of Yin on the effects of modifications for sgRNAs are highly relevant in that the instantly claimed invention is reciting sgRNAs, which will then have the same RNA-RNA and RNA-protein interactions required for activity. As such, Yin teaches that 2’-O-Me modifications in the upper stem region are judicious chemical modifications specifically for activity of sgRNAs in complex with Cas9 proteins, wherein Yin identified regions of sgRNA that tolerate chemical modification without inhibiting the interaction of Cas9 and sgRNA and while maintaining or enhancing genome editing activity [pg 1180 col 1 ¶ 3].
Regarding Applicant’s argument 4), as discussed in the Office Action mailed 24 April 2025, the teachings of Ryan present two alternative sgRNAs with identical nucleotide sequences and mutually exclusive modifications for entries 174 and 177. Ryan Table 3 indicates that 174 is modified at the G and A residues, whereas 177 is modified at the C and U residues. Ryan Table 4 teaches that the % target cleaved for 174 is 85%, but that the % target cleaved for 177 is 0%. However, Table 4 also teaches that the % cleaved vs the control is identical for both 174 and 177 at 84%. As such, the teachings of Ryan are mixed and/or contradictory on the efficacy of the 177 construct. Further, the example of one ineffective modification pattern provided by Ryan does not eliminate the teachings of Yin and Mir which provide examples of modified sgRNAs with multiple modification patterns which promote both cleavage efficiency and stability, thereby providing alternatives which are easier to synthesize than unmodified sgRNAs, and which they show improve targeting at multiple distinct target sequences. As such, the teachings of Ryan do not obviate the teachings and motivations provided by Yin to incorporate 2’-O-Me modifications in the upper stem loop nucleotides at all of the upper stem loop nucleotides.
Regarding Applicant’s argument 5), note that sgRNA constructs used to teach the motivation for 8 or all of the nucleotides of the upper stem loop to comprise 2’-O-Me modifications did not themselves comprise 2’F modifications, neither are 2’F modifications taught by May nor recited in the instant claims. Further, 2’F modifications are not likely to affect the secondary structure of the sgRNA in the same way that deleting residues will affect the structure. As such, teachings that 2’F modifications may adversely affect the structure of the sgRNAs is not relevant to the instant rejection. As discussed above, May teaches the deletion of residues from the hairpin region as claimed, along with any corresponding structural changes, and so Yin is not relied on for teaching the deletion of such residues. As discussed above and in the prior action, Yin teaches sgRNAs comprising 2’-OMe modifications at either eight or every nucleotide of the stem loop (e.g., 2’OMe_loops, SG-2’OMe, and SG-2’OMe-PS) have the highest efficiency of all tested modification variants and also have higher efficiency than the unmodified sgRNA [Figure 1], even wherein only the upper stem and hairpin 1 region comprise 2’-OMe modifications. Note again, as discussed above, that independent claim 1 as written does not require any hairpin 1 nucleotides present in the sgRNA to be unmodified. Additionally, the motivation to modify those nucleotides to improve stability and ease of manufacture is not relevant wherein those nucleotides are not present and further would not dissuade an ordinarily skilled artisan from applying the teachings that stabilizing the upper stem not only does not inhibit activity but actually improves it.
Additionally, note that the upper stem region itself does not interact with the hairpin 1 region nor do the upper stem and hairpin 1 regions interact with the same amino acids of the Cas9 protein, as taught by each of Yin Figures 1, 3 and Wang Figures 3-4, wherein the sgRNA structure is overlayed with the Cas9 interacting domains schematically, and by Yin’s teaching that “[t]hese structural biology studies demonstrated that the tetraloop and the second stem-loop of sgRNA extend outside of the Cas9 protein” [pg 1180 col 2 ¶ 2]. The lack of interactions between the tetraloop/upper stem region and the step loop 2/hairpin 1 region is also demonstrated by the crystal structure of a Cas9-sgRNA-target DNA ternary complex [Nishimasu et al. 2014, Cell, 156, 935-949, IDS, Figure 1, 2]. As such, there is no reason for an ordinarily skilled artisan to assume that the lack of disrupted sgRNA activity arising from stabilization of the upper stem loop would depend upon simultaneous stabilization of the hairpin 1 region.
Yin further teaches that they hypothesized that the tetraloop/upper stem region and second step-loop/hairpin 1 could tolerate modifications in all nucleotides, as long as those modification did not inhibit loop formation, and further teaches that the sgRNA carrying the 2’ OMe (the “2’Ome, Loops” construct) modification at those two loops was functional, and showed a small but significant increase of editing efficiency [pg 1180 col 2 ¶ 2]. Yin also teaches that 2’F modification decreased the activity of sgRNA in cells, which lead them to focus on 2’ OMe modifications for the invariable part of the sgRNA during their subsequence studies [pg 1180 col 2 ¶ 2], thereby providing motivation specifically for 2’-OMe modification. Yin also teaches to avoid 2’ modifications for nucleotides which interact with Cas9 protein at the 2’ hydroxyl group, which does not include the upper stem or hairpin 1 region. Accordingly, Yin provides motivation to modify the upper stem loop with 2’ OMe modifications without teaching away from applying the stabilizing 2’ OMe modifications to a sgRNA which has 5-10 nucleotides of the hairpin 1 region deleted. As such, an ordinarily skilled artisan at the time of filing the instant application would have been motivated to modify the upper stem region with 2’OMe modifications to increase stability of the loop region such that it would have been prima facie obvious to an ordinarily skilled artisan at the time of filing the instant application to modify the sgRNA of May, wherein May teaches that deletion of the hairpin 1 nucleotides increases cleavage efficiency, with the 2’Ome modifications taught by Yin to increase the stability and ease of manufacturing of the sgRNA with a reasonable expectation of success.
Therefore, Applicant’s amendments and arguments do not overcome a finding of obviousness under 35 U.S.C. 103 over May, Yin, Wang, and Mir, and the rejection is maintained.
The rejection of amended claim 469 under 35 U.S.C. 103 as being unpatentable over May et al. [US20150376586A1, IDS, published 31 December 2015, cited in a prior office action]; in view of Yin et al. [2017, Nature Biotechnology, 35(12), 1179-1187, IDS]; Wang et al. [2017, Chemical Reviews, Vol. 117, 9874-9906, cited in a prior office action]; and Mir et al. [2018, BioRxiv [preprint], deposited 28 March 2018, cited in a prior action] as applied to amended, previously presented, and original claims 1, 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, and 471-474 above; and further in view of Dombrowski [US20200354702A1, published 12 November 2020, with priority to U.S. Provisional Application No. 62/566,144, filed 29 September 2017]; is maintained. Applicant's amendments to the claims and arguments have been fully considered but have not been found persuasive in overcoming the rejection for reasons of record as discussed in detail below.
Applicant amended claim 469 for clarity without altering the scope of the claims sufficiently to overcome a finding of obviousness under 35 U.S.C. 103 over May, Yin, Wang, and Mir.
Applicant argues that Dombrowski does not remedy the defects of May, Yin, Wang, and Mir as applied to claim 1 above, and so the rejection of claim 469 should be withdrawn. However, that is not agreed.
As discussed above, Applicant’s amendments and arguments have not overcome a finding of obviousness under 35 U.S.C. 103 over May, Yin, Wang, and Mir as applied to claims , 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, and 471-474 above. Accordingly, Applicant’s arguments have not overcome a finding of obviousness for dependent claim 469 under 35 U.S.C. 103 over May in view of Yin, Wang, and Mir, and further in view of Dombrowski, and the rejection is maintained.
Double Patenting
The rejection of amended, previously presented, and original claims 1, 5, 13-14, 16, 25, 97, 437, 443, 452-458, 463-466, 469, and 471-473 on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 34-36, 39, 41-42, 46, 48, 56, 58-64, 70-72, 79-81, and 86-89 of copending Application No. 17/836,265, hereafter referred to as the ‘265 application, in view of May et al. [US20150376586A1, IDS, published 31 December 2015]; is withdrawn in view of the ‘265 application claims amendment filed 27 May 2026, such that independent claim 1 now recites that the hairpin 1 region consists of a sequence selected from any one of AGAGCU, AGAAAU, CGAAAG, AAAAU, AAAGU, ACAGU, CAAG, or AAAU, which are within the scope of instant claim 1 as written, but are not encompassed by the elected species of SEQ ID NO: 302.
Conclusion
No claim is allowed.
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DR. KATIE L. PENNINGTON
Examiner
Art Unit 1634
/KATIE L PENNINGTON/Examiner, Art Unit 1634
Dr. A.M.S. Wehbé
/ANNE MARIE S WEHBE/Primary Examiner, Art Unit 1634
