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 .
Applicant’s response of 08/05/2026 has been received and entered into the application file.
Claims 1, 4, and 12 were amended in the claim set filed 08/05/2026.
Claim 11 was canceled in the claim set filed 08/05/2026.
Accordingly, claims 1, 3, 4, 7, and 12 are pending and under consideration.
Status of Prior Objections/Rejections
RE: Claim Rejections - 35 USC § 101 and 35 USC § 112(b)
►Claims 1, 3, 4, 7, and 11-12 were previously rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
►Claims 1, 3, 4, 7, and 11-12 were also previously 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.
The cancellation of claim 11 renders the rejection thereof moot.
The amendments to instant claim 1 (from which all other claims depend) have obviated the basis of the rejection of record. The rejection of record is hereby withdrawn.
RE: Claim Rejections - 35 USC § 112(a)
►Claims 11 and 12 were previously rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The cancellation of claim 11 renders the rejection thereof moot.
The amendments to instant claim 12 have obviated the basis of the rejection of record. The rejection of record is hereby withdrawn.
RE: Claim Rejections - 35 USC § 103
►Claims 1, 3, 4, and 7 were previously rejected under 35 U.S.C. 103 as being unpatentable over WO 03/052071 (hereinafter Glazer; of record) in view of WO 2016/132129 A1 (hereinafter Rothwell; of record), as evidenced by Aggarwal, 1995 (hereinafter Aggarwal; of record).
Applicant has traversed the rejection of record, indicating that amended instant claim 1 requires introducing into a cell a pre-formed synthetic nucleic acid delivery vector comprising a closed circular single stranded DNA having a duplex and a loop containing a donor template, and cleaving the duplex within the delivered vector at a recognition sequence using a nuclease to release the donor template intracellularly. Applicant further asserts that Glazer does not disclose or suggest this features, instead disclosing systems in which nucleic acid constructs such as plasmids or viral vectors are delivered into cells and subsequently undergo significant multi-step intracellular processing to generate several structures on the way to generating a single-stranded DNA. Per Applicant, the stem-loop structures relied upon in the rejection of record arise as intermediates during intracellular processing, rather than pre-formed delivery vectors introduced into the cell. In summary, Applicant asserts that Glazer does not teach introducing a pre-formed closed circular single stranded DNA delivery vector having the claimed duplex-loop architecture, instead relying upon intracellular generation of nucleic acid intermediate structures.
Applicant further asserts that Rothwell does not cure the deficiencies of the system outlined in Glazer, as Rothwell discloses many structures, one of which is a circular vector with a stem loop. Per Applicant, Rothwell does not point towards the use of a circular DNA with a hairpin as a delivery vector for donor DNA per se.
In response, this is not found persuasive. While the Examiner acknowledges that Glazer is drawn to a vector system designed to produce single-stranded DNA in cells, Glazer explicitly discloses that Figure 1C (previously cited) depicts a structure with an internal stem-loop that is cleaved by MboII to release the loop as an ssDNA containing the insert sequence (Example 1), as previously set forth. Additionally, as previously set forth, Rothwell discloses that covalently closed DNA structures prevent attack by enzymes such as exonucleases (page 47, lines 3-6). Per MPEP § 2141(II)(C), “a person of ordinary skill in the art is also a person of ordinary creativity, not an automaton” KSR, 550 U.S. at 421, 82 USPQ2d at 1397. Based on the state of the art at the time of filing, the Examiner asserts that a person of ordinary skill in the art (also a person of ordinary creativity) would have therefore been motivated to circumvent the preparatory steps disclosed in Glazer to streamline delivery of an insert sequence via the structure taught therein, wherein said structure is covalently closed as per Rothwell. Additionally, while it is acknowledged that Glazer discloses intracellular generation of said structure, this generation broadly reads on introducing the same into a cell, as the structure is indeed introduced into the cell and will function the same in the cell regardless of whether it was generated intracellularly or supplied exogenously.
Accordingly, Applicant’s arguments are not found persuasive. However, the amendments to the instant claim set have necessitated amended grounds of rejection, which are set forth in detail below.
►Claims 11 and 12 were previously rejected under 35 U.S.C. 103 as being unpatentable over WO 03/052071 (hereinafter Glazer; of record) in view of WO 2016/132129 A1 (hereinafter Rothwell; of record), as evidenced by Aggarwal, 1995 (hereinafter Aggarwal; of record) as applied to claim 1 above, and further in view of Wang et al., 2015 (hereinafter Wang; of record).
The cancellation of claim 11 renders the rejection thereof moot.
Applicant has traversed the rejection of record, asserting that the substitution of Cas9 for restriction enzymes is not a routine modification, as Cas9 requires specific targeting mechanisms and operates differently from restriction enzymes.
In response, this is not found persuasive. The disclosure of Wang establishes that Cas9 can be programmed to assume the role traditionally performed by restriction enzymes. While this modification may not be routine, the disclosure of Wang nonetheless establishes that it is possible and confers several advantages, including speed and convenience (abstract; page 161, column 1, paragraph 1-page 161, column 2, paragraph 1; page 170, column 1, paragraph 1).
Accordingly, Applicant’s arguments are not found persuasive. However, the amendments to the instant claim set have necessitated amended grounds of rejection, which are set forth in detail below.
New/Maintained Grounds of Objection/Rejection
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 12 is 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.
Claim 12 recites the limitation "the guided nuclease" (bolded emphasis added) in line 2. There is insufficient antecedent basis for this limitation in the claim. It would be remedial to amend the instant claim language such that there is sufficient antecedent basis for each and every claim term, for example by reciting “the method of claim 1, wherein the nuclease is a Cas9 or a variant thereof capable of cleaving the duplex to release the linear single stranded donor template.”
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 3, 4, and 7 are rejected under 35 U.S.C. 103 as being unpatentable over WO 03/052071 (hereinafter Glazer; of record) in view of WO 2016/132129 A1 (hereinafter Rothwell; of record) and Pahle and Walther, 2016 (hereinafter Pahle), as evidenced by Aggarwal, 1995 (hereinafter Aggarwal; of record).
With regard to amended instant claim 1, which recites “a method of providing a linear single stranded donor template to a cell for genome editing, comprising
introducing into a cell a delivery vector, wherein the delivery vector is a synthetic nucleic acid delivery vector comprising a closed circular single stranded DNA, said vector comprising:
a duplex formed from a first section and a third section of said DNA, said sections including sequences which are complementary;
a loop formed from a second section of said DNA, said section separating the first and third sections;
wherein said duplex includes a recognition sequence for a targeted nuclease, wherein said vector delivers a linear single stranded DNA, wherein said single stranded DNA is present within the second section and wherein said linear single stranded DNA is a donor template; and
cleaving the duplex at the recognition sequence with the nuclease to release the linear single stranded donor template,”
as previously set forth, Glazer discloses means for delivery of providing large quantities of donor DNA for recombination (page 4, lines 1-3), including methods for intracellularly generating single stranded DNA molecules that can induce a chromosomal event such as recombination, wherein said recombination may provide a functional copy of a mutated target gene (page 4, lines 5-7; page 4, lines 23-30). Such single stranded DNA molecules are known to mediate targeted genome modification via induced recombination (page 2, line 25-page 3, line 2) and are therefore useful for gene therapy (page 3, lines 10-12). Glazer explicitly discloses that the single stranded DNA molecules taught therein are recombined into a target chromosomal sequence (page 14, lines 4-5; Example 4) and further that such nucleic acids and/or the vectors to generate them intracellularly may be delivered via a variety of mechanisms, including liposomal delivery (page 14, lines 30-31) and viral vector delivery (page 15, lines 9-10). The single stranded DNA molecules taught in Glazer include that shown in Figure 1C, which has a double stranded stem-single stranded loop structure (page 5, lines 29-31; Figure 1C) and reads on the instantly claimed structure. This nucleic acid structure is further processed by cleavage with MboII to yield a linear ssDNA product of interest released from within the loop (page 6, lines 7-9; page 18, lines 24-25; Figure 1D). As is known to those of ordinary skill in the art, restriction enzymes such as MboII are by definition highly specific in acting exclusively on their recognition sites (reviewed in Aggarwal: see page 11, column 1, paragraph 2), meaning the MboII disclosed in Glazer reads on the instantly claimed targeted nuclease acting on a recognition sequence for purposes of releasing the therapeutic, linear, single stranded DNA within the construct taught therein and instantly claimed. Furthermore, as set forth above, Glazer discloses that the nucleic acid constructs taught therein are for targeted insertion into the genome, as instantly claimed, and that such constructs may be delivered (i.e. via liposomes) or produced intracellularly following delivery via a viral vector. Thus, Glazer discloses a method of providing a linear single stranded donor template to a cell for genome editing, wherein said linear single stranded donor template is provided within a nucleic acid construct that may be delivered via liposomal delivery of said nucleic acid construct, as instantly claimed. While Glazer does not teach introduction of the structure of Figure 1C into a cell, Glazer teaches intracellular generation of the same (see entire reference), which may be broadly considered to read on introduction of the structure into a cell. Furthermore, as set forth above, per MPEP § 2141(II)(C), “a person of ordinary skill in the art is also a person of ordinary creativity, not an automaton” KSR, 550 U.S. at 421, 82 USPQ2d at 1397. Based on the state of the art at the time of filing, the Examiner asserts that a person of ordinary skill in the art (also a person of ordinary creativity) would have therefore been motivated to circumvent the preparatory steps disclosed in Glazer to streamline delivery of an insert sequence via the structure taught therein, wherein said structure is covalently closed as per Rothwell and set forth below.
This deficiency is cured by Rothwell. Rothwell discloses that single-stranded circular DNA molecules have particularly utility as therapeutic agents when they are closed structures, as the covalently closed structure prevents attack by enzymes such as exonucleases (page 47, lines 3-6). Therefore, someone of ordinary skill in the art would be motivated by the disclosure of Rothwell to covalently close the structure disclosed to be delivered for purposes of inserting a donor construct at a target site in the genome of Glazer, as set forth in greater detail below.
However, even if one does not accept that the disclosures of Glazer and Rothwell render the amended claim set obvious regarding the introduction of the vector into the cell, this deficiency is cured by Pahle. Pahle discloses that dumbbell-shaped vectors (which comprise 2 hairpins and a stem) deliver linear, covalently closed DNA as in the instant application (Table 2; Section 3.3). Per Pahle, this structure is routinely transfected into cells as a minimal vector with high clinical potential for nonviral gene therapies (Section 3.3). While the dumbbell-shaped vectors disclosed in Pahle are structurally distinct from the instantly claimed vector, both dumbbell-shaped vectors and the instantly claimed vector comprise a stem and a loop, wherein said structure is covalently closed. A person of ordinary skill in the art would therefore reasonably predict that the vector collectively disclosed by Glazer and Rothwell (i.e. a covalently closed delivery vector comprising a stem and a loop) would also be capable of being introduced into the cell for purposes of nonviral gene therapy, as disclosed in Pahle.
With regard to claim 3, which recites “the method [of claim 1] provides a linear single stranded donor template to a cell for gene editing,” as set forth above, Glazer explicitly discloses that the single stranded DNA molecules taught therein are recombined into a target chromosomal sequence (page 14, lines 4-5; Example 4; Figure 2). Such target chromosomal sequences include the locus for TK genes (Example 3). Thus, Glazer discloses a method of providing a linear single stranded donor template to a cell for gene editing, as instantly claimed. Specifically, digestion of the stem-loop structure with MboII as set forth above releases the ssDNA loop of SEQ ID NO: 5 (Figure 1), which then inserts into the targeted gene locus as shown in Figure 2. Thus, it is considered that Glazer discloses each and every additional limitation of amended claim 3.
With regard to amended claim 4, which recites “the linear single stranded donor template [of the method of claim 1] has a free 5’ and 3’ end once released from the delivery vector,” as depicted in Figures 1C-1D of Glazer, digestion with MboII yields ssDNA with 5’ and 3’ ends that are recombined into a target site in the genome, as depicted in Figure 2 of Glazer. Furthermore, given that the structure of Figure 1C of Glazer in view of Rothwell is identical to the instantly claimed structure and is processed in the same manner as is instantly claimed, both the structure of Glazer/Rothwell and the instantly claimed structure must have free 5’ and 3’ ends once released from the delivery vector construct carrying the template sequence (see MPEP § 2114 and § 2173.05(g)).
With regard to claim 7, which recites “the method of claim 1, wherein the nuclease binds to the recognition sequence without a guide,” as set forth above, Glazer discloses that cleavage of the stem-loop structure taught therein with MboII yields a linear ssDNA product released from the sequence of interest contained in the loop (page 6, lines 7-9; page 18, lines 24-25; Figure 1D). Additionally, as is known to those of skill in the art, restriction endonucleases, by definition, are highly specific in acting on their recognition sites without the assistance of a guide (reviewed in Aggarwal: see page 11, column 1, paragraph 2). Thus, it is considered that Glazer discloses each and every additional limitation of amended claim 7.
Given that Glazer discloses delivery (i.e. via liposomes) of nucleic acid constructs taught therein (including that of Figure 1C, which reads on the instantly claimed construct with the exception of it being a closed circular structure) for release of ssDNA for targeted genome integration (i.e. for therapeutic purposes), that Rothwell discloses that covalently closed circular ssDNA structures are more better suited to in vivo use due to being less vulnerable to attack by exonucleases, and that Pahle discloses cellular delivery of nonviral, minimal gene therapy vectors comprising a stem and a loop (i.e. dumbbell vectors), it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the nucleic acid construct delivered as in Glazer to be a covalently closed circular structure (as disclosed in Rothwell and Pahle) to predictably deliver a covalently closed circular ssDNA structure with a duplex formed from a first and third section and a loop formed from a second section (the delivery of which is disclosed in Pahle) such that the ssDNA loop is released via MboII digestion for targeted genome integration (i.e. at the TK locus as disclosed in Glazer). One would have been motivated to make such a modification in order to receive the expected benefit of delivering therapeutic nucleic acid constructs that are not vulnerable to attack by exonucleases and that are capable of integrating into the genome at a targeted site.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over WO 03/052071 (hereinafter Glazer; of record) in view of WO 2016/132129 A1 (hereinafter Rothwell; of record) and Pahle and Walther, 2016 (hereinafter Pahle), as evidenced by Aggarwal, 1995 (hereinafter Aggarwal; of record) as applied to claim 1 above, and further in view of Wang et al., 2015 (hereinafter Wang; of record).
The combined disclosures of Glazer, Rothwell, and Pahle (as evidenced by Aggarwal) are described above and applied as before. However, these disclosures do not teach the guided nuclease (i.e. Cas9) of instant claim 12.
With regard to amended claim 12, which recites the “the nuclease [of the method of claim 1] is…Cas9 or a variant thereof capable of cleaving the duplex to release the linear single stranded donor template,” as set forth above, Glazer, Rothwell, and Pahle collectively disclose the method of amended instant claim 1. However, Glazer only discloses the use of targeted nucleases such as restriction enzyme MboII (Figures 1C and 1D). This deficiency is cured by Wang. Wang discloses that Cas9 can be used like a restriction enzyme to cleave DNA without the limitations of the more commonly used restriction enzymes (page 170, column 1, paragraph 1). Per Wang, Cas9 is a guided nuclease that can be programmed as desired to cleave almost anywhere with high stringency (abstract), as opposed to cleavage by restriction enzymes, the activity of which is constrained by their defined recognition sequences, which may themselves be present multiple times in a large vector (page 161, column 1, paragraph 1-page 161, column 2, paragraph 1). This usage of Cas9 confers several advantages to researchers, including speed and convenience (page 170, column 1, paragraph 1).
Given the disclosed success of Wang in programming Cas9 to assume the role traditionally performed by restriction enzymes, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to cleave the duplex stem of the circularized structure disclosed by Glazer, Rothwell, and Pahle with Cas9 (as disclosed in Wang) rather than the restriction enzymes disclosed in Glazer to predictably cleave the duplex DNA stem to release the single-stranded loop with flexible sequence targeting and high stringency. One would have been motivated to make such a modification in order to receive the expected benefit of cleaving the duplex DNA stem (to release the single-stranded loop for targeted genome integration) with greater targeted sequence flexibility and high stringency, thereby delivering the single-stranded loop for targeted genome integration, as disclosed in Examples 3 and 4 of Glazer.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 Sarah E Allen whose telephone number is (571)272-0408. The examiner can normally be reached M-F 8-5.
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/SARAH E ALLEN/ Examiner, Art Unit 1637
/J. E. ANGELL/ Primary Examiner, Art Unit 1637
