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 .
Election/Restrictions
Applicant’s election of Group ll (Claim 19) drawn to a population of double stranded MuA substrates for modifying a template polynucleotide in the reply filed on 06/04/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Amendments and Status of the Claims
This action is in response to papers filed 16 June 2026 in which claims 1-5, 8, 10, 12-17, and 20-25 are canceled, and new claims 27-36 are added. All of the amendments have been thoroughly reviewed and entered.
Claims 19, and 27-36 are under prosecution.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 08/14/2023 and 06/04/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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.
Claim(s) 19 and 27-36 is/are rejected under 35 U.S.C. 103 as being unpatentable over Heron et. al. (WO2015110813, effectively filed: 1/22/15-- IDS REF 8/14/23) in view of Kavanagh et. al. (US20130017978A1, effectively filed 7/9/12 – IDS REF 8/14/23).
Regarding claim 19, Heron teaches a method for attaching one or more polynucleotide binding proteins to a target polynucleotide and methods for characterizing target polynucleotides (Abstract). A double stranded polynucleotide may be contacted with a MuA transposase and a population of double stranded MuA substrates, wherein a proportion of the substrates in the population are Y adaptors bound to one or more polynucleotide binding proteins (pg.65. par. 2/ lines 5-8). Each substrate in the population comprises at least one overhang of universal nucleotides such that the transposase fragments the template polynucleotide and ligates a substrate to one or both ends of the double stranded fragments (pg.65, par. 3/ lines 17-20). Heron further teaches that one or more helicases may be attached to the MuA substrate Y adaptors (i.e. loading moieties) before they are contacted with the double stranded polynucleotide and MuA transposase (pg.66, par.3, lines 14-18).
Regarding claim 27, Heron teaches that each substrate in the population preferably comprises at least one overhang of universal nucleotides such that the transposase fragments the template polynucleotide and ligates a substrate to one or both ends of the double stranded fragments (pg.65, par. 3, lines 17-19).
Regarding claim 28, Heron teaches that at least a portion of the polynucleotide is double stranded (pg.15, par.3/Lines 11-12) and the polynucleotide may be any length. For example, the polynucleotide can be at least 10, at least 50, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400 or at least 500 nucleotides in length (pg. 15, par. 6/ Lines 28-30).
Regarding claim 29, Heron teaches the double stranded portion has a length up to 10 kb (pg.81, par.1/lines 1-2).
Regarding claim 30, Heron teaches the double stranded portion comprises a dinucleotide comprising deoxycytidine (dC) and deoxyadenosine (dA) at the 3’ end of each strand (pg.14, par. 6/ lines 27-29).
Regarding claims 32 and 33, Heron teaches that the overhang is preferably five nucleotides in length (pg.65, par. 3/line 23).
Regarding claim 34, Heron teaches that each substrate comprises an overhang at both ends of one strand and the overhang at the 5’ end is formed from universal nucleotides (pg. 65, par. 3, lines 17-18). Regarding claim 35, Heron teaches that the translocase is a helicase (pg. 15, par. 7, line 32).
Regarding claim 36, Heron teaches the helicase may be derived from a Hel308 helicase, a RecD helicase, such as TraI helicase or a TrwC helicase, a XPD helicase or a Dda helicase (pg.20, par. 3, line 35- pg.21, par.1, line 1).
Regarding claim 31, Kavanagh teaches a method of generating DNA fragmentation libraries based on a transposition reaction in the presence of a transposon end with an engineered cleavage site providing facilitated downstream handling of produced DNA fragments ([0002]). Transposon complexes form between a transposase enzyme and a fragment of double stranded DNA that contains a specific binding sequence for the enzyme, termed “transposon end” ([0030]). For MuA transposase, this sequence is 50 bp long (SEQ ID NO. 1) ([0026]). SEQ ID NO: 1 taught by Kavanagh is identical to SEQ ID NO: 94 of the instant application, indicated in the alignment below.
SEQ ID 1 of US/13544054 compared to SEQ ID 94
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75
674
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It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have taken the teachings of Heron to combine with the teachings of Kavanagh to incorporate a MuA transposon sequence shown in SEQ ID NO: 94 on each of the double strand substrates in order to initiate formation of a transposition complex (Kavanagh, [0026]) and ultimately produce a plurality of shorter, modified double-stranded polynucleotides from a template double stranded polynucleotide.
Conclusion
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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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571) 272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/A.H.B./Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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