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 .
Priority
Acknowledgment is made of applicant’s claim for priority based on a provisional application filed as 63/142,990 on 01/28/2021.
All claims are given the priority date of 01/28/2021.
Application Status
Receipt is acknowledged of amendment, filed 05/21/2026.
Claim Objections
The numbering of claims is not in accordance with 37 CFR 1.126 which requires the original numbering of the claims to be preserved throughout the prosecution. When claims are canceled, the remaining claims must not be renumbered. When new claims are presented, they must be numbered consecutively beginning with the number next following the highest numbered claims previously presented (whether entered or not).
Misnumbered claims 36-54 have been renumbered 35-53.
Therefore, claims 12, 17, 20, 24, 25, 29, 34-36, 40-41, 43, 46 and 48-53 are currently pending.
Election/Restriction
Applicant's election with traverse of Group I, drawn to claims 12, 17, 20, 24, 25 and 46-48, in the reply filed on 05/21/2026 is acknowledged. The traversal is on the ground(s) that Group II, drawn to claims 29 and 34 (claims 27 and 28 are cancelled) all depend from the independent claim 12 and thus encompass the same subject matter as claim 12, which is within the Group I claims. Applicant’s arguments regarding withdrawing the restriction requirement between Group I and II are persuasive in view of Applicant’s amendments to the claims filed on 05/21/2026. Therefore, claims 29 and 34 will be examined with Group I.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement with regards to the restriction between Group I and III, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 35, 36, 40, 41 and 43 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 05/21/2026.
Claims 12, 17, 20, 24, 25, 29, 34, 46 and 48-53 are currently under examination.
Information Disclosure Statement
Receipt of acknowledgment of the information disclosure statements filed on 10/27/2023, 08/07/2024, 05/21/2026 have been received and all references have been considered.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 12, 17, 20, 24, 46 and 48-53 are rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by Doudna et al (WO 2021/155020 A2; with priority to 62/968,644 with a date of 01/31/2020) as evidenced by Zhang et al (WO 2020/236972 A2).
Regarding claim 12, Doudna teaches a transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites (Page 1, Abstract; Page 65, Fig. 1 and Page 100, Fig. 10B). Doudna teaches the RNA-guided CRISPR-Cas transposase wherein the gRNA complexes with the Cas protein [0006-0007, 00219 and 00264]. Doudna teaches that the transposon encodes TnsB, TnsC and TniQ proteins within the vector (Page 100, Figure 10B). Doudna teaches the Cas protein is a Cas12k as identified in SEQ ID NO: 24 which is 100% identical to instant SEQ ID NO: 1 (Page 74, Figure 6F and See Appendix I). Zhang is only cited to show that TniA is also known as TnsB, TniB is also known as TnsC and TniQ is also known as TnsD; and therefore, in certain embodiments these Tn5053 transposase subunits may be referred to as TnsB, TnsC, and TnsD [0626].
Regarding claim 17, Doudna teaches the guide RNA is a dual-molecule guide RNA referred to as sgRNA comprising the crRNA and the tracrRNA within a single molecule RNA [0093-0095].
Regarding claims 20 and 24, Doudna teaches an all-in-one conjugate vector additionally comprising a donor polynucleotide comprising a payload sequence for insertion, such as gentamicin resistance gene (GmR) cassette flanked by the transposon left end and transposon right end (Page 100, Fig. 10B).
Regarding claim 46, Doudna teaches an all-in-one conjugate vector comprises a transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites additionally comprising a donor polynucleotide comprising a payload sequence for insertion, such as gentamicin resistance gene (GmR) cassette flanked by the transposon left end and transposon right end (Page 1, Abstract; Page 65, Fig. 1 and Page 100, Fig. 10B).
Regarding claim 48, Doudna teaches the all-in-one conjugate vector comprises a transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites additionally comprising a donor polynucleotide comprising a payload sequence for insertion, such as gentamicin resistance gene (GmR) cassette flanked by the transposon left end and transposon right end were further delivered to E. coli cells [00248].
Regarding claims 49-51, the claim is interpreted that “a nucleotide sequence” means two or more consecutive nucleotides and not the entirety of the sequence.
Doudna teaches the guide RNA sequence of SEQ ID NO: 6 which is 100% identical to two or more consecutive nucleotides of instant SEQ ID NO: 5 ([0095] and See Appendix II). Doudna teaches the guide sequence has complementarity with (hybridizes to) a target sequence of the target DNA and wherein the ShCasTn gRNAs used 23 nt spacers and a 5' -GTT Cas 12k PAM [0090 and 00226].
Regarding claim 52, a kit is a collection of items and therefore, since the reference teaches all of the listed items, then it teaches the kit.
Doudna teaches a transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites (Page 1, Abstract; Page 65, Fig. 1 and Page 100, Fig. 10B). Doudna teaches the RNA-guided CRISPR-Cas transposase wherein the gRNA complexes with the Cas protein [0006-0007, 00219 and 00264]. Doudna teaches that the transposon encodes TnsB, TnsC and TniQ proteins within the vector (Page 100, Figure 10B). Doudna teaches the Cas protein is a Cas12k as identified in SEQ ID NO: 24 which is 100% identical to instant SEQ ID NO: 1 (Page 74, Figure 6F and See Appendix I). Zhang is only cited to show that TniA is also known as TnsB, TniB is also known as TnsC and TniQ is also known as TnsD; and therefore, in certain embodiments these Tn5053 transposase subunits may be referred to as TnsB, TnsC, and TnsD [0626]. Doudna teaches an all-in-one conjugate vector additionally comprising a donor polynucleotide comprising a payload sequence for insertion, such as gentamicin resistance gene (GmR) cassette flanked by the transposon left end and transposon right end (Page 100, Fig. 10B). Doudna teaches the guide RNA sequence of SEQ ID NO: 6 which is 100% identical to two or more consecutive nucleotides of instant SEQ ID NO: 5 ([0095] and See Appendix II). Doudna teaches the guide sequence has complementarity with (hybridizes to) a target sequence of the target DNA and wherein the ShCasTn gRNAs used 23 nt spacers and a 5' -GTT Cas 12k PAM [0090 and 00226].
Regarding claim 53, a kit is a collection of items and therefore, since the reference teaches all of the listed items, then it teaches the kit. The claim is interpreted as a list that can comprise the list in its entirety or not due to the use of the phrase “and/or”.
Doudna teaches a transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites (Page 1, Abstract; Page 65, Fig. 1 and Page 100, Fig. 10B). Doudna teaches the RNA-guided CRISPR-Cas transposase wherein the gRNA complexes with the Cas protein [0006-0007, 00219 and 00264]. Doudna teaches that the transposon encodes TnsB, TnsC and TniQ proteins within the vector (Page 100, Figure 10B). Doudna teaches the TnsB sequence as SEQ ID NO: 21 which is 100% identical to instant SEQ ID NO: 2 and the TnsC sequence as SEQ ID NO: 29 which is 100% identical to instant SEQ ID NO: 3 (Page 73, Fig. 6C and Page 77, Fig. 6K; and See Appendix III and IV, respectively).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over Doudna et al (WO 2021/155020 A2; with priority to 62/968,644 with a date of 01/31/2020) in view of Kholodii et al (Mol Microbiol. 1995 Sep;17(6):1189-200).
The teachings of Doudna are as described and applied as above.
Regarding claim 29, Doudna teaches a transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites (Page 1, Abstract; Page 65, Fig. 1 and Page 100, Fig. 10B). Doudna teaches the RNA-guided CRISPR-Cas transposase wherein the gRNA complexes with the Cas protein [0006-0007, 00219 and 00264]. Doudna teaches that the transposon encodes TnsB, TnsC and TniQ proteins within the vector (Page 100, Figure 10B). Doudna teaches the TnsB sequence as SEQ ID NO: 21 which is 100% identical to instant SEQ ID NO: 2 and the TnsC sequence as SEQ ID NO: 29 which is 100% identical to instant SEQ ID NO: 3 (Page 73, Fig. 6C and Page 77, Fig. 6K; and See Appendix III and IV, respectively).
Doudna does not teach the sequence of TniQ as instant SEQ ID NO: 4.
Kholodii teaches the TniQ protein in cascade with TniA and TniB for the use as a transposon system wherein the sequence of TniQ is 100% identical to instant SEQ ID NO: 4 (Page 1189, Abstract; and See Appendix V).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the TniQ protein of Doudna to include the specific TniQ protein sequence as taught by Kholodii because Doudna teaches it is within the ordinary skill in the art to use the transposon encodes TnsB, TnsC and TniQ proteins within the transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites and Kholodii teaches the TniQ protein sequence that is 100% identical to instant SEQ ID NO: 4 and capable of use in the transposon system with TniA and TniB.
One would have been motivated to make such a substitution in order to receive the expected benefit of the specific TniQ protein sequence as taught by Kholodii.
Claim 34 is rejected under 35 U.S.C. 103 as being unpatentable over Doudna et al (WO 2021/155020 A2; with priority to 62/968,644 with a date of 01/31/2020) in view of Sternberg et al (US 2020/0283769 Al).
The teachings of Doudna are as described and applied as above.
Regarding claim 34, Doudna does not teach that any of the protein used are purified proteins.
Sternberg teaches a DNA segment encoding the present protein(s) is contained in a plasmid vector that allows expression of the protein(s) and subsequent isolation and purification of the protein produced by the recombinant vector and accordingly, the proteins disclosed herein can be purified following expression from the native transposon, obtained by chemical synthesis, or obtained by recombinant methods [0332]. Sternberg teaches all the transposon proteins (TniA, TniB and TniQ) are recombinantly expressed and purified individually, and RNA-guided DNA integration is later reconstituted by mixing the proteins in vitro together with gRNA [0719].
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the TniA protein, TniB protein and TniQ protein of Doudna to include the purified TniA, TniB and TniQ proteins as taught by Sternberg because Doudna teaches it is within the ordinary skill in the art to use the transposon encodes TnsB, TnsC and TniQ proteins within the transposon system comprising: i) a nucleotide sequence encoding polypeptides that form a CRISPR-associated transposase complex; ii) a nucleotide sequence encoding a guide RNA: and iii) a transposon, or an insertion site for a transposon, flanked by CAST complex recognition sites and Sternberg teaches the TniA, TniB and TniQ proteins were purified proteins used in a transposon system in conjugation with a Cas protein and sgRNA.
One would have been motivated to make such a substitution in order to receive the expected benefit of the purified proteins from the native transposon system as taught by Sternberg.
Allowable Subject Matter
Claim 25 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
No claims are allowed.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/CELINE X QIAN/Primary Examiner, Art Unit 1637
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