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 .
Please note that the examiner for this application has changed. Please address future correspondence to Avanda Harvey-Butler (Art Unit 1683) whose telephone number is (571) 272-6511.
This Office Action is in reply to Applicants’ correspondence of 10/20/2025.
Applicants’ remarks and amendments have been fully and carefully considered
but are not found to be sufficient to put the application in condition for allowance. Any
new grounds of rejection presented in this Office Action are necessitated by Applicants’
amendments. Any rejections or objections not reiterated herein have been withdrawn in light
of the amendments to the claims or as discussed in this Office Action.
This Action is made FINAL.
Claim Status
Claims 1, 8, 9, and 21 have been amended.
Claim 17 has been cancelled.
Claims 1-3, 6-16, 19, 21, and 23-25 are currently pending.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 10/20/2025 was filed after the mailing date of the Non-Final Office Action on 04/18/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Withdrawn Objection to the Specification
The objection to the disclosure as set forth on page 2 of the Office Action of 04/18/2025 is withdrawn in light of the amendment to the specification provided by applicant in the reply of 10/20/2025, which is entered.
Withdrawn Rejections
The rejection of claims 8, 9, 17, and 21 under 112 (b) as being indefinite is withdrawn in view of applicant’s amendments and cancellation of claim 17.
The rejection of claims 1, 6-9, 14-17, 21 and 23 under 35 U.S.C. 102(a)(2) as
being anticipated by Drmanac (US PG PUB 2009/0011943, US Patent Doc 007 on
IDS dated 09/15/2024) are withdrawn in view of applicant’s amendment of independent claim 1.
The rejection of claims 1, 6, 14-17 and 23 under 35 U.S.C. 102(a)(2) as being
anticipated by Elf (WO 2016/007063, foreign patent doc 005 on IDS dated
09/15/2024) are withdrawn in view of applicant’s amendment of independent claim 1.
Claim Rejections - 35 USC § 112- NEW Necessitated by Amendment
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 1 is 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.
This is a new matter rejection necessitated by the amendments.
Claim 1 (upon which claims 2-3, 6-16, 19, and 21 depend) is amended to recite “directly ligating.” A review of the specification yields only one teaching of “direct” ligating, which is describes in paragraph 0078 of the instant specification as applying only to the 5’ end of the target sequence. Because the claim also encompasses embodiments where the ‘3 end of the target can be directly ligated, the amendment constitutes new matter.
Additionally, Pattanayak et al teaches direct ligation (Figure 1), in accordance with the definition provided in paragraph 0078 of the instant specification because the PAM sequence is present at the 3’ end of the target sequence (page 839, column 1). Thus, the claim has been given the broadest reasonable interpretation consistent with the teachings of the specification regarding “directly ligating” (In re Hyatt, 211 F.3d1367, 1372, 54 USPQ2d 1664, 1667 (Fed. Cir. 2000): see MPEP 2111).
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.
Claim 3 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 3 recites the limitation "the endonuclease is a restriction enzyme ". There is insufficient antecedent basis for this limitation in the claim. Amended claim 1 in which claim 3 depends on, does not mention an endonuclease.
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.
Claims 2-3 are 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. Claims 2 and 3 contain the limitation " Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), Zinc Finger Nucleases (ZFN), and Transcription activator like effector nucleases (TALENs)” for the target nucleic acid (claim 2) and restriction enzyme of the endonuclease (claim 3). The instant claims are written to encompass a scope that is broader than the amended limitation, “(a) contacting a sample comprising a plurality of non-circularized nucleic acids to a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas system protein-gRNA complex…”, of independent claim 1. 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.
Claim Rejections - 35 USC § 102- MAINTAINED
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.
Claims 1-3, 6, 7,19, 21 and 23-25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pattanayak et al (High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature biotechnology, 2013, 31(9) 893-843).
Regarding claim 1, Pattanayak et al teaches a method of contacting a non-circular nucleic acid sample with an endonuclease to cleave it at a target location (e.g., Pattanayak et al., page 840, Fig 1 part a), ligating the nucleic acid to form circular target nucleic acid, hybridizing at least one primer to the circular target nucleic acid, amplifying the target nucleic acid via rolling circle amplification and sequencing the amplified nucleic acid (e.g., Pattanayak et al., page 840 Fig 1 part b), reading on the limitations: “A method of determining a nucleic acid sequence, comprising:(a) contacting a sample comprising a plurality of non-circularized nucleic acids to a Clustered Regulatory Interspaced Short Palindromic Repeat (CRISPR)/ Cas system protein-gRNA complex to cleave a target nucleic acid among the plurality of non-circularized nucleic acids; (b) directly ligating the target nucleic acid to form a circular target nucleic acid; (c) hybridizing at least one primer to the circular target nucleic acid; (d) amplifying the circular target nucleic acid through rolling circle amplification to generate an amplified nucleic acid; and (e) sequencing the amplified nucleic acid” of the instantly rejected amended claim 1.
Regarding claim 2, Pattanayak teaches the method of claim 1, wherein the target nucleic acid comprises at least one of a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) recognition sequence (e.g., Pattanayak et al., page 840, fig 1).
Regarding claim 3, Pattanayak teaches the method of claim 1, wherein the endonuclease is a restriction enzyme specific to at least one site on the target nucleic acid, Clustered Regulatory Interspaced Short Palindromic Repeat (CRISPR)/Cas system protein-gRNA complex (e.g., Pattanayak et al., page 840, fig 1).
Regarding claim 6, Pattanayak teaches the method of claim 1, wherein the primer is selected from random primer (e.g., Pattanayak et al., page 840, fig 1; TempliPhi™ manual).
Regarding claim 7, Pattanayak teaches the method of claim 1, wherein the endonuclease cleaves the target nucleic acid to form a free 5' end and a free 3' end of the target nucleic acid (e.g., Pattanayak et al., page 840, fig 1b).
Regarding claim 19, Pattanayak teaches the method of claim 1, wherein the sequencing is a next-generation sequencing (e.g., Pattanayak et al., title; abstract).
Regarding claim 21, Pattanayak teaches the method of claim 1, wherein ligating the target nucleic acid is performed using a single stranded splint, wherein the single stranded splint comprises sequences complementary to the ends of the target nucleic acid (e.g., Pattanayak et al., pg. 844, left col. para 4).
Regarding claim 23, Pattanayak teaches a method of preparing a nucleic
acid for sequencing, comprising (a) contacting a sample comprising a plurality of nucleic
acids to an endonuclease to cleave a target nucleic acid among the plurality of nucleic
acids; (b) ligating the target nucleic acid sequence to form a circular target nucleic acid;
(c) hybridizing at least one primer to the circular target nucleic acid; and (d) amplifying the circular target nucleic acid through rolling circle amplification (e.g., Pattanayak et al.,
page 840 Fig1(a-b); page 844, left column, para 4; TempliPhi™ manual).
Regarding claim 24, Pattanayak teaches the method of claim 23, wherein the nucleic acid comprises at least one of a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) sequence (e.g., Pattanayak et al., page 840 fig 1).
Regarding claim 25, Pattanayak teaches the method of claim 23, wherein the
endonuclease is a restriction enzyme specific to at least one site on the nucleic acid,
Clustered Regulatory Interspaced Short Palindromic Repeat (CRISPR)/Cas system
protein-gRNA complex (e.g., Pattanayak et al., page 840, fig 1).
Claim Rejections - 35 USC § 103 MODIFIED- Necessitated by Amendment
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 8-9 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Pattanayak et al (High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature biotechnology, 2013, 31(9) 893-843). as applied to claim 1 above, and further in view of Drmanac (US PG PUB 2009/0011943, US Patent Doc 007 on IDS dated 09/15/2024).
The method of claim 1 is taught by Pattanayak et al. as discussed above.
Pattanayak does not teach hybridizing a first primer and a second primer to the target nucleic acid, or contacting the sample with an exonuclease that does not degrade the circular target nucleic acid where the rolling circle amplification is performed in situ, but this was commonly known in the art and taught by Drmanac.
Regarding claim 8, Drmanac teaches hybridizing, a first primer to the target nucleic acid, wherein a first primer comprises at least one sequence complementary to at least a portion of the sequence of the free 5’ end and to at least a portion of the sequence of the free 3’ end of the target nucleic acid (e.g., Drmanac fig 1c, 1612).
Regarding claim 9, Drmanac teaches hybridizing a first primer and a second primer to the target nucleic acid, wherein a first primer comprises at least one sequence complementary to at least a portion of the 5’ end and the 3’ end of the target nucleic acid, and wherein a second primer comprises a sequence that is complementary to a portion of the target nucleic acid that is not adjacent to the 5’ end or the 3’ end of the linear target nucleic acid (e.g., Drmanac fig 1c, 1612).
Regarding claim 14, Drmanac teaches the sample with an exonuclease (e.g., Drmanac para 0308).
Regarding claim 15, Drmanac teaches the exonuclease does not degrade the circular target nucleic acid (e.g., Drmanac para 0308).
Regarding claim 16, Drmanac teaches the rolling circle amplification is performed in situ on the circular target nucleic acid (e.g., Drmanac para 0185).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teaching of Pattanayak to include the teachings of Drmanac to incorporate an exonuclease in a method of determining a nucleic acid sequence, for the benefit of removing linear DNA molecules from the ends of the DNA fragments ([0308]). The methods of Drmanac allow the identification of entire target sequences (Abstract).
Claims 10, 12, and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Pattanayak et al (High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature biotechnology, 2013, 31(9) 893-843). and Drmanac ( US PG PUB 2009/0011943, US Patent Doc 007 on IDS dated 09/15/2024) as applied to claims 8-9 and 14-16 above, and further in view of Cao et al (Scaffolding and completing genome assemblies in real-time with nanopore sequencing, 2016, 8(1), 14515) and Slotko et al (Overview of next-generation sequencing technologies, 2018, 112(1), e59).
The teachings of Pattanayak and Drmanac are discussed above.
Pattanayak and Drmanac fail to teach the use of nanopore sequencing nor concurrent amplification and sequencing or a predetermined threshold for sequencing, but these were known in the art and taught by Cao et al and Slotko et al.
Regarding claim 10, Cao teaches sequencing amplified nucleic acid comprises performing a nanopore sequencing analysis (e.g., Cao et al, title).
Regarding claim 12, Slotko teaches the steps of amplifying and sequencing are performed concurrently (e.g., Slotko et al., page 4, para 4; page 4, last para; page 5, para 1; page 6, para 2).
Regarding claim 13, Slotko teaches the steps of amplifying and sequencing are performed concurrently (e.g., Slotko et al., page 4, para 4; page 4, last para; page 5, para 1; page 6, para 2), and Cao et al teaches a method wherein the sequencing is performed until a pre-determined minimum required quality of sequence of a template is achieved (e.g., Cao et al., abstract).
It would have been prima facie obvious before the effective filing date of the
claimed invention for a person having ordinary skill in the art to have used the method of
Cao to perform nanopore sequencing until a predetermined threshold of quality is
reached with the method of sequencing of Pattanayak. The skilled artisan would have
been motivated to use the method of Cao et al based on the teachings of Cao et al, that
in other methods, sequencing analysis is conducted only after sequencing is complete,
resulting in variable and low-quality results, whereas their method is terminated only
when the quality metric is reached (e.g., Cao et al., abstract). Thus, the use of the
predetermined threshold in nanopore sequencing of Cao et al, with the high-throughput DNA sequencing method of Pattanayak (e.g., Pattanayak et al., abstract) would have been a simple combination of prior art elements to yield predictable results.
It would have been prima facie obvious before the effective filing date of the
claimed invention for a person having ordinary skill in the art to have used the method of
amplification and sequencing in the same phase of Slotko et al with the method of
sequencing of Pattanayak. The skilled artisan would be motivated to combine steps to
save time. Where the prior art teaches different protocols for achieving high quality
sequencing results, a person of ordinary skill has good reason to pursue known options
within their technical grasp for optimization of their method of sequencing. If this leads
to anticipated success, it is likely the product not of innovation, but of ordinary skill and
common sense to provide routine optimization.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Pattanayak et al (High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nature biotechnology, 2013, 31(9) 893-843) and Cao et al (2016) as applied to claim 10 above, and further in view of Garalde et al (2018).
Regarding claim 11, the method of claim 10 is discussed above.
Neither Pattanayak et al. nor Cao et al. teach the adaptor of motor protein.
Regarding claim 11, Garalde teaches the primer comprises an adaptor that binds to a motor protein used in the nanopore sequence analysis (e.g., Garalde et al., page 207, left column, para 4; right column, para 1).
It would have been prima facie obvious before the effective filing date of the
claimed invention for a person having ordinary skill in the art to have used the adaptor associated motor protein of Garalde with the method of nanopore sequencing of Pattanayak in view of Cao et al. The skilled artisan would have been motivated to use the method of Garalde et al based on the teachings of Garalde et al, that their method is compatible with very long reads and is strand specific (e.g., Garalde et al., page 204, right column, para 3), both of which can improve overall data quality. Thus, the use of the adaptor specific motor proteins of Garalde et al with the sequencing method of Pattanayak in view of Cao et al would have been a simple combination of prior art elements to yield predictable results.
Response to Arguments
Applicant's arguments filed 10/20/2025 have been fully considered but they are not persuasive.
Applicant argues the method of Pattanayak et al recites “Synthetic 5’- phosphorylated, 53-base oligonucleotides were self-ligated into circular single-stranded DNA in vitro.” (Pattanayak, pg.840) Accordingly, failing to teach the limitations of amended claim 1: “(a) contacting a sample comprising a plurality of non-circularized nucleic acids to a Clustered Regulatory Interspaced Short Palindromic Repeat (CRISPR)/ Cas system protein-gRNA complex to cleave a target nucleic acid among the plurality of non-circularized nucleic acids.” And then later “directly ligating the target nucleic acid to form a circular target nucleic acid.”
Figure 1b of Pattanayak teaches an in vitro selection protocol with a non-circular DNA oligonucleotide that undergoes circular ligation and rolling-circle amplification to generate concatemeric DNA libraries that were incubated with sgRNA: Cas9 complexes, teaching the limitations of instant claim 1.
Pattanayak et al teaches a method of contacting a non-circular nucleic acid sample with an endonuclease to cleave it at a target location (e.g., Pattanayak et al., page 840, Fig 1 part a), ligating the nucleic acid to form circular target nucleic acid, hybridizing at least one primer to the circular target nucleic acid, amplifying the target nucleic acid via rolling circle amplification and sequencing the amplified nucleic acid (e.g., Pattanayak et al., page 840 Fig 1 part b). Furthermore, Figure 1 and page 893 of Pattanayak et al. clearly illustrates “directly ligating” based on paragraph 0078 of the instant specification as discussed in the rejection above.
Applicant's arguments regarding the previous rejections under 102(a)(2) as being anticipated by Drmanac and Elf have been considered and withdrawn in view of applicant’s amendment of independent claim 1.
Applicant’s remaining arguments rely on alleged deficiencies previously addressed, which are unpersuasive for the reasons discussed above. Therefore, the claims remained rejected based on the prior art citations presented in the rejections.
Conclusion
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 Avanda Harvey-Butler whose telephone number is (571)272-6511. The examiner can normally be reached M-F, 9-5 ET.
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/A.H.B./ Examiner, Art Unit 1683
/Robert T. Crow/ Primary Examiner, Art Unit 1683
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