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 .
Application Status
Applicant’s response filed May 4, 2026, including remarks and amendments to the claims and specification, is acknowledged. Claims 1-2, 6, 13, 17, 20-21, 23, and 39-41 were amended, and claims 4, 16, 19, and 22 were cancelled. Claims 1-2, 6-11, 13-14, 17, 20-21, 23-25, 27, 29, 31-34, 36, 38-48, and 50-51 are pending.
Restriction/Election
Claims 42-48, and 50-51 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention. Claims 1-2, 6-11, 13-14, 17, 20-21, 23-25, 27, 29, 31-34, 36, 38-41 are under examination hereinafter.
Priority
Applicant's priority claims to Application Nos. 62/952,981 and PCT/US2020/066949 are acknowledged. The claims under examination find support in Application No. 62/952,981, and therefore, have an effective filing date of December 23, 2019.
Withdrawn Rejections
Applicant’s remarks and amendments have been considered. The amendments to the claims are sufficient to overcome the § 101 rejections of claims 39-41. Specifically, the term “isolated” is interpreted to mean a cell removed from an environment, e.g., removed from a human organism (see [01034]). Likewise, the phrase “non-human organism, or tissue, or organ,” excludes human organisms, or tissues, or organs. The amendments to claim 1 to require that the one or more programmable DNA nucleases are “a RNA-guided DNA nuclease, a Zinc Finger nuclease, a TALE nuclease (TALEN), or a meganuclease” are sufficient to overcome the remaining § 101 rejections raised in the prior action. Finally, Applicant’s amendments to claim 1 to require the limitations of claim 22 (now cancelled), are sufficient to overcome the § 102 rejections raised over Zymergen in the prior action. These rejections are withdrawn, accordingly.
Applicant’s remarks and amendments are not sufficient to place the claims in condition for allowance for the reasons that follow. Any objection or rejection not reiterated herein has been overcome by amendment.
Specification
The specification is objected to because of the following informalities:
The disclosure is objected to because it contains embedded hyperlinks and/or other forms of browser-executable code. The embedded hyperlinks and/or other form of browser-executable code are in at least paragraphs [0260], [0474], [0480], [0581], [0673], [0821], [0935], [0952], [01088], [01093]. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of terms which are trade names or marks used in commerce, has been noted in this application, i.e., “Lipofectamine 2000” ([0539]). Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks. The terms should be accompanied by the generic terminology; furthermore, the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Appropriate correction is required.
Claim Objections
Claims 6, 13, and 21 are objected to because of the following informalities:
Claim 6 recites “wherein the one or more programmable DNA nuclease is a CRISPR-Cas system.” Based on the specification, a CRISPR-Cas system refers to “transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated (“Cas”) genes, including sequences encoding a Cas gene, a tracr… sequence… a tracr-mate sequence… a guide sequence… or other sequences and transcripts from a CRISPR locus” ([0111]). The term “one or more programmable DNA nucleases” recited in claim 1 is interpreted as encompassing agents with DNA cleaving function (e.g., “a protein or small molecule”), or non-functional nucleases derived therefrom (e.g., dead Cas proteins). See at least [0097] and [0181]. Based on these definitions, it is reasonably clear that claim 6 intends for the one or more programmable DNA nucleases to be one or more Cas polypeptides, which are the elements of a CRISPR-Cas system which comprise DNA cleaving function. This conclusion is further supported by several dependent claims (e.g., “wherein one or more of the one or more Cas polypeptides…,” in claim 7). It would be preferable, therefore, to amend claim 6 to recite “wherein the one or more programmable DNA nucleases are one or more Cas polypeptides
This claim will be interpreted hereinafter as in the suggested amendment above.
Claim 13 recites “a first target sequence of a target polynucleotide.” Claim 1 recites “a target polynucleotide,” and it is reasonably clear that the target polynucleotide in claim 13, refers to the target polynucleotide in claim 1. It would be preferable to amend claim 13 to recite “a first target sequence of [[a]] the target polynucleotide.”
Claim 21 recites “the optional second guide molecules.” It is reasonably clear that this refers to the “second guide molecule” of claim 13. It would be preferable to amend claim 21 to recite “the optional second guide molecule[[s]],” accordingly.
Appropriate correction is required.
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 24 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. The rejection that follows is maintained from the prior action.
Claim 24 recites “the first, or optional second guide molecule,” but no such first or optional second guide molecule are explicitly required, implied by, or inherent to claim 1 from which the claim depends. These elements lack sufficient antecedent basis in the claim.
In the interest of compact prosecution, claim 24 will be interpreted as depending from claim 13, which provides basis for the aforementioned limitations.
Response to Remarks - 35 USC § 112(b)
Applicant’s remarks regarding the § 112(b) rejections raised in the prior action have been reviewed. Applicant’s remarks do not specifically address the § 112(b) rejection over claim 24 raised in the prior action, which is maintained above.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 40 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. The rejection that follows is new and necessitated by Applicant’s amendments to the claims.
Claim 40 recites “The cell of claim 39, wherein the cell is an isolated cell, optionally, a human cell….” Claim 39 is already directed to “[a]n isolated cell,” and the remaining elements in claim 40 (i.e., “a human cell, a non-human animal cell”) are not required due to the term “optionally.” Thus, claim 40 fails to further limit the subject matter of the claim upon which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Notice to Joint Inventors
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.
Claim Rejections - 35 USC § 103 – Zymergen in view of Kennedy
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.
Claims 1-2, 6-11, 13-14, 17, 20-21, 23-25, 27, 29, 31-34, 36, 38-41 are rejected under 35 U.S.C. 103 as being unpatentable over Zymergen (DeLoache et al., WO 2018/013990 A1, published 18 January 2018; of record) in view of Kennedy (Kennedy et al., 2 March 2017, US 2017/0058298 A1; of record). The rejections that follow are new and necessitated by Applicant’s amendments to the claims.
Regarding claim 1, Zymergen teaches an engineered composition for modifying polynucleotides, the composition comprising: one or more programmable DNA nucleases which are an RNA-guided DNA nuclease (e.g., "Cpf1," "Cas9"); and one or more ligases, wherein each ligase is covalently or non-covalently attached to a complex with one or more of the one or more DNA nucleases (“the present disclosure teaches fusing a Cpf1 or other CRISPR polypeptide with a polypeptide with ligase activity,” "In some embodiments, a linker is used to genetically fuse an enzymatic ligase to a Cpf1 or other Targetable Enzyme gene to create an engineered, non-naturally occurring protein," "Fusion of protein subunits of a complex has been performed on other systems and can be accomplished ... by one skilled in the art with knowledge of the nucleic acid sequences to be fused to the Cas9 or Cpf1," [0123]-[0130]; "enzymatic ligases, include, but are not limited to, bacteriophage T4 ligase, T7 ligase ... Afu ligase," [120]; “the present disclosure teaches methods and compositions… methods of gene editing using any targetable DNA nuclease (e.g., Cpf1, Cas9…), [0102]; “Persons skilled in the art will immediately recognize that the aforementioned references to vectors encoding Cpf1 endonucleases are equally applicable to other CRISPR endonucleases or Targetable Enzymes,” [0180]).
Zymergen does not teach a “splint oligonucleotide,” wherein the term “splint” is interpreted as referring to an intended use for the oligonucleotide, and wherein the oligonucleotide is interpreted as any oligonucleotide which could be used as a “splint” between the target polynucleotide and donor molecule, i.e., an oligonucleotide which “comprises a region capable of hybridizing to a cleaved strand of a target polynucleotide and a region capable of hybridizing to a donor molecule.”
However, Kennedy teaches splint oligonucleotides (“adaptor segment”) designed to “tether[] [] the guide RNA to polynucleotide sequences that can act as donors for homologous recombination (donor polynucleotides)” ([0038]-[0066]). Kennedy teaches that the splint oligonucleotides comprise a region capable of hybridizing to a donor sequence in a donor molecule, and a region capable of hybridizing to a target sequence (“the adaptor segment of the guide RNA comprises ssDNA or ssRNA adapted for hybridizing to a polynucleotide (e.g., a donor polynucleotide…) through Watson Crick base-pairing,” [0044]; Fig. 3-4; “the crRNA segment comprises a guide sequence that is capable of hybridizing to a target sequence,” [0068]-[0078]). Kennedy teaches that the splint oligonucleotides result in non-covalent attachment of the DNA nuclease (i.e., Cas protein) to the donor molecule comprising the donor sequence (“When loaded with the guide RNA:donor polynucleotide complex, the Cas protein will bring the donor polynucleotide to a target cleavage site,” [0039]). See also Fig. 4-6 which illustrate a Cas protein complexed with a gRNA comprising an adaptor segment, wherein the adaptor segment is attached to a donor molecule.
Kennedy teaches use of the splint oligonucleotides in CRISPR-Cas genome editing strategies similar to that of Zymergen (see at least Fig. 4-6; [0017]; [0129]-[0138]). Kennedy teaches that “[h]omologous gene targeting approaches have been used… for gene correction, and in theory, for the correction of mutations linked with monogenic diseases. However, this application is difficult, due to the low efficiency of the process” ([0007]; [0005]). Kennedy teaches that splint oligonucleotides “increase[] the local concentration of donor polynucleotide around the Cas cleavage site and increases the likelihood that a homologous recombination (HR) event will occur” ([0039]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have included a splint oligonucleotide taught by Kennedy in an engineered composition of Zymergen. It would have amounted to a simple combination of a known element usable in methods of CRISPR-Cas genome editing, with a known composition for CRISPR-Cas genome editing, by known means to yield predictable results. The design and synthesis of splint oligonucleotides, and their combination with compositions comprising DNA nucleases, was known in the art as evidenced by Kennedy. The skilled artisan would have expected Kennedy’s splint oligonucleotide and Zymergen’s engineered composition to have the same functions described by the respective references when combined; the splint oligonucleotide would tether the donor molecule to the gRNA, and thereby, increase the local concentration of the donor molecule and efficiency of its integration at the target polynucleotide by the elements in the composition of Zymergen. The skilled artisan would have been motivated to arrive at the claimed engineered composition because Zymergen and Kennedy are both concerned with site-specific insertion of donor sequences via CRISPR-Cas strategies, and Kennedy teaches an element which is likely to improve the efficiency of these methods.
Regarding claims 6-10, Zymergen teaches the one or more programmable DNA nucleases are one or more Cas polypeptides, wherein the one or more Cas polypeptides are a Cas9 polypeptide or Cas12 polypeptide, which is referred to as “Cpf1” throughout Zymergen (“the present disclosure teaches fusing a Cpf1 or other CRISPR polypeptide with a polypeptide with ligase activity,” "In some embodiments, a linker is used to genetically fuse an enzymatic ligase to a Cpf1 or other Targetable Enzyme gene to create an engineered, non-naturally occurring protein," "Fusion of protein subunits of a complex has been performed on other systems and can be accomplished ... by one skilled in the art with knowledge of the nucleic acid sequences to be fused to the Cas9 or Cpf1," [0123]-[0130]; “methods of gene editing using any targetable DNA nuclease (e.g., Cpf1, Cas9…), [0102]; “Persons skilled in the art will immediately recognize that the aforementioned references to vectors encoding Cpf1 endonucleases are equally applicable to other CRISPR endonucleases or Targetable Enzymes,” [0180]).
Regarding claims 2 and 11, Zymergen teaches the one or more Cas polypeptides is a nickase (“the systems and methods disclosed herein can be used with… Cas9 mutants that act as single stranded nickases,” [0112]).
Regarding claim 13, Zymergen teaches the engineered composition further comprises a guide molecule (“the present disclosure teaches methods and compositions of vectors, constructs, and nucleic acid sequences encoding the gene editing complexes of the present disclosure,” [0167]; “the plasmids and vectors of the present disclosure will encode for the Cpf1 protein(s) and also encode the crRNA and/or donor insert sequences,” [0169]; Fig. 1). Zymergen teaches the guide molecule forms a complex with an RNA-guided DNA nuclease and comprises a guide sequence capable of directing site-specific binding to a first target sequence in a target polynucleotide (Fig. 1).
Regarding claim 14, Zymergen teaches a first target sequence on a first strand of a double stranded target polynucleotide, and a second target sequence on a second strand of the double stranded target polynucleotide (Figs. 2, 4). As shown in Fig. 2 and 4, the first and second target sequences define an intervening target region for insertion of a donor sequence. Zymergen also teaches methods with such a first and second target sequence (Fig. 7).
Regarding claim 17, Zymergen teaches the engineered composition further comprises a donor molecule comprising a donor sequence configured for insertion into a target polynucleotide (“the plasmids and vectors of the present disclosure will… also encode the crRNA and/or donor insert sequences of the present disclosure,” [0169]). Zymergen teaches donor sequences which are double-stranded DNA (see Fig. 2 and 4, which illustrate a donor insert sequence with two strands).
Regarding claim 20, Kennedy teaches that the splint oligonucleotide results in non-covalent attachment of the DNA nuclease (i.e., Cas protein) to the donor molecule comprising the donor sequence (“When loaded with the guide RNA:donor polynucleotide complex, the Cas protein will bring the donor polynucleotide to a target cleavage site,” [0039]). See also Fig. 4-6 which illustrate a Cas protein complexed with a gRNA comprising an adaptor segment, wherein the adaptor segment is attached to a donor molecule. The combination rendered obvious above meets the limitations of claim 20.
Regarding claim 21, the “region” comprises the features of the splint oligonucleotide of claim 1. The claim, therefore, is interpreted as encompassing a composition comprising a guide molecule, wherein the guide molecule comprises a region comprising the “splint oligonucleotide,” which comprises “a region capable of hybridizing to a cleaved strand of the target polynucleotide and a region capable of hybridizing to the donor molecule.” See at least FIG. 1 of the instant specification for a guide molecule comprising such a region, wherein the region corresponds to a splint oligonucleotide.
Kennedy teaches a guide molecule comprising the splint oligonucleotide (“the adaptor segment of the guide RNA comprises ssDNA or ssRNA adapted for hybridizing to a polynucleotide (e.g., a donor polynucleotide…) through Watson Crick base-pairing,” [0044]; Fig. 3-4). As described above, the splint oligonucleotide of Kennedy comprises a region capable of hybridizing to a donor sequence in a donor molecule, and a region capable of hybridizing to a target sequence (“the adaptor segment of the guide RNA comprises ssDNA or ssRNA adapted for hybridizing to a polynucleotide (e.g., a donor polynucleotide…) through Watson Crick base-pairing,” [0044]; Fig. 3-4; “the crRNA segment comprises a guide sequence that is capable of hybridizing to a target sequence,” [0068]-[0078]). The combination rendered obvious above meets the limitations of claim 21.
Regarding claim 23, Zymergen teaches the donor sequence is configured to insert a gene or gene fragment at one or multiple copies of the target polynucleotide (“GOI,” Fig. 2; “repair fragment,” “Reconstituted gene (e.g., marker/GFP/etc),” Fig. 4).
Regarding claim 24, Zymergen teaches the one or more ligases are each covalently or non-covalently attached to at least one of the programmable DNA nucleases (“the present disclosure teaches fusing a Cpf1 or other CRISPR polypeptide with a polypeptide with ligase activity,” [0128]; “In some embodiments, a linker is used to genetically fuse an enzymatic ligase to a Cpf1 or other Targetable Enzyme gene,” [0129]).
Regarding claims 25 and 27, Zymergen teaches the ligase “is an enzymatic ligation reagent or catalyst that, under appropriate conditions, forms phosphodiester bonds between the 3’-OH and the 5’-phosphate of adjacent nucleotides in DNA molecules, RNA molecules, or hybrids” ([0123]). Thus, Zymergen teaches one or more ligases which are capable of ligating a single-strand break. Zymergen also teaches that the ligase is used to “sew” DNA back together ([0121]). See also Zymergen’s examples comprising ligation of double-strand breaks (Fig. 2, 4, and 7). Thus, Zymergen also teaches one or more ligases which are capable of ligating a double-strand break.
Regarding claim 29, Zymergen teaches that the sequence encoding a ligase is linked at the 3’ end or 5’ end of a sequence encoding a programmable DNA nuclease ([0130]). The skilled artisan would understand that the 3’ end and 5’ ends of the sequences referred to by Zymergen correspond to N- and C-termini of the encoded protein. Thus, Zymergen teaches that the one or more ligases are fused to a C- or N-terminus of a programmable DNA nuclease.
Regarding claim 31, Zymergen teaches the one or more programmable DNA nucleases comprises one or more nuclear localization signals ([0136]-[0138]).
Regarding claims 32-33, Zymergen teaches a vector composition comprising one or more vectors comprising nucleic acid sequences encoding one or more components of the engineered composition ([0087]; [0167]-[00180]; [0187]-[0190]). Zymergen teaches “single vector” compositions, which is interpreted as one vector, e.g., a plasmid, encoding one or more components of the engineered composition (“introducing into the cell, one or more vectors encoding for…,” “introducing into the cell a CRISPR complex encoded in one or more vectors,” see at least embodiments 12-18, and 22-26.1 on pgs. 20-21).
Regarding claim 34, Zymergen teaches viral vectors encoding one or more components of the engineered composition (“Vectors can be… viruses,” [0087]; “persons having skill in the art will recognize that viral vectors or plasmids for gene expression can be used to deliver the complexes herein,” [0179]).
Regarding claims 36 and 38, Zymergen teaches delivery compositions comprising one or more components of the engineered composition of claim 1, and a delivery vehicle, wherein the delivery vehicle comprises ribonucleoproteins (“Virus-like particles (VLP) can be used to encapsulate ribonucleoprotein complexes or recombinant expression, and purified ribonucleoprotein complexes disclosed herein can be purified and delivered to cells via electroporation or injection,” [0179]).
Regarding claims 39-40, Zymergen teaches an isolated cell comprising the engineered composition of claim 1, or a vector composition comprising one or more vectors encoding one or more components of the engineered composition of claim 1 (“the present disclosure teaches methods for getting exogenous protein (Cpf1 and DNA ligase), RNA (crRNA), and DNA (target DNA to be ligated into the genome”) into the cell… Various methods for achieving this have been described previously including direct transfection of protein/RNA/DNA or DNA transformation followed by intracellular expression of RNA and protein,” [0176]; [0179]-[0180]; “In some embodiments, the vectors of the present disclosure may be introduced into the host cells using any of a variety of techniques,” [0174]; “host cell (e.g., bacteria, yeast cell, fungal cell, CHO, human cell, etc.,” [0071]; “In some embodiments, viable genome-editing tools must be delivered to the nucleus of eukaryotic cells,” [0137]).
Regarding claim 41, Zymergen also teaches non-human organisms comprising the cell (“In yet other embodiments, the genome-editing tools of the present disclosure are used in organisms without nuclei,” [0137]).
Response to Remarks - 35 USC § 103
Applicant’s remarks regarding the § 103 rejections raised in the prior action have been reviewed. Applicant alleges that Kennedy “does not disclose a splint oligonucleotide as a discrete independent composition element.” Applicant argues that “Claim 1 now requires a splint oligonucleotide as a standalone compositional element – a discrete, independent molecular component separate from both the guide molecule and the donor sequence….” Applicant states that “Kennedy’s “adaptor segment” is an integral, internal segment of the guide RNA molecule itself, designed to hybridize to a donor polynucleotide and tether it to the guide and thereby indirectly to the Cas protein.” Applicant alleges that the rejection “reads a structural limitation out of the claim.”
Examiner respectfully disagrees with Applicant’s interpretation of the claim, upon which these arguments are based. The claim requires “a splint oligonucleotide comprising a first region capable of hybridizing to a cleaved strand of a target polynucleotide and a second region capable of hybridizing to a donor sequence.” These limitations are interpreted as any oligonucleotide (i.e., any two or more consecutive nucleotides), which could be used as a “splint,” and is capable of hybridizing to a cleaved strand of a target polynucleotide, and capable of hybridizing to a donor sequence. There are no limitations in this phrase, or in claim 1 as a whole, which exclude splint oligonucleotides which are integral, internal components of a guide RNA molecule, or of any other nucleotide sequence. Indeed, claim 21, encompasses a guide molecule comprising a “region” which comprises the features of the splint oligonucleotide, and as such, has been interpreted herein as encompassing a guide molecule comprising a region comprising the splint oligonucleotide. This is a reasonable interpretation based on FIG. 1 and the specification as further described below.
The specification also does not exclude splint oligonucleotides which are integral, internal components of a guide RNA molecule, or of any other nucleotide sequence. On the contrary, the specification specifically provides examples of splint oligonucleotides which are integral, internal components of a guide RNA molecule. See FIG. 1 which depicts a “splint-gRNA,” paragraph [0094] which states that “the guide RNA can further include… a splint sequence capable of facilitating ligation between a separate donor sequence and a non-target strand of a target polynucleotide,” and paragraph [0154] which states that “the bridge or splint region is present at the 3’ end of the guide molecule and/or 5’ end of a guide molecule.” Applicant’s remarks with respect to the splint oligonucleotide rely upon subject matter which is not claimed. Kennedy’s splint oligonucleotide meets the required elements of claim 1. Applicant’s remarks with respect to the splint oligonucleotide are not persuasive.
Applicant also submits that “claim 20 requires that the donor sequence is covalently or non-covalently attached to one of the programmable DNA nucleases.” Applicant alleges that “Kennedy teaches a Cas-guide-donor complex in which the donor hybridizes to an adaptor segment on the guide RNA, which is itself loaded into Cas. The donor is attached to the guide RNA, not directly to the nuclease.” Applicant alleges that the rejection “reads a meaningful structural limitation out” of the claim.
Examiner respectfully disagrees with Applicant’s interpretation of the claim, upon which these arguments are based. The claim requires “attachment” which is interpreted as “covalent or non-covalent interaction between two or more molecules” ([0247]). The manner of attachment is not limited. The claim encompasses virtually any means of attachment which results in the “interaction” between the donor sequence and the one or more programmable DNA nucleases. Neither the claim nor specification specifically exclude indirect attachment between the donor sequence and the one or more programmable DNA nucleases. Indeed, as shown in FIG. 1, attachment of the donor sequence (“Insert DNA”) through hybridization between an adaptor segment on the guide RNA (“splint-gRNA”), which is itself loaded into a Cas protein (“Cas9”), is within the scope of the invention. Applicant’s remarks with respect to the attachment between the donor sequence and the one or more programmable DNA nucleases relies upon subject matter which is not claimed. Kennedy meets the required elements in claim 1. These remarks are also not persuasive.
Applicant submits that “Examiner has not provided an articulated rationale with rational underpinning for combining [the references].” Applicant alleges that the references teach “fundamentally different DNA modification strategies, and no teaching or evidence supports the proposition that Kennedy’s HDR-tethering approach would improve the efficiency of DeLoache’s ligation-based system.”
Examiner respectfully disagrees that Kennedy and Zymergen (“DeLoache”) teach fundamentally different DNA modification strategies. As stated in the prior action and above, “Zymergen and Kennedy are both concerned with site-specific insertion of donor sequences via CRISPR-Cas strategies.” As stated in the prior action, “Kennedy teaches that splint oligonucleotides “increase[] the local concentration of donor polynucleotide around the Cas cleavage site and increases the likelihood that a homologous recombination (HR) event will occur” ([0039]). As stated in the prior action, the skilled artisan would have recognized that Kennedy and Zymergen were both concerned with site-specific insertion of donor sequences via CRISPR-Cas strategies, and, based on the teachings of Kennedy, recognized that a splint oligonucleotide would likely improve the efficiency of Zymergen’s methods because it would tether the donor molecule to the gRNA, and thereby, increase the local concentration of the donor molecule and integration efficiency at the target polynucleotide by the elements in the composition of Zymergen. Applicant has provided no evidence, aside from argument, that the references could not be combined as described in the prior action and above. The rejection meets each element required of MPEP 2143(I)(A). Applicant’s remarks with respect to the alleged fundamental differences of Kennedy and Zymergen, or the alleged deficiencies of the rejection are not found persuasive.
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 JENNA L PERSONS whose telephone number is (703)756-1334. The examiner can normally be reached M-F: 9-5pm.
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/JENNA L PERSONS/Examiner, Art Unit 1637
/Soren Harward/Primary Examiner, TC 1600
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