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 without traverse of Group II in the reply filed on January 13, 2026 is acknowledged.
Claims 1-7 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on January 13, 2026.
Information Disclosure Statement
The IDS received on November 8, 2022 is proper and is being considered by the Examiner.
Drawings
The drawings received on November 8, 2022 are acceptable.
Claim Rejections - 35 USC § 112
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.
Claims 10-16 are 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 11 is indefinite for the following reasons.
Claim 11 (by dependency through claim 10) recites the step of preparing a nucleic acid-adapter molecule complex where an adapter molecule directly or indirectly binds to at least one portion of the nucleic acid to be analyzed and inhibits the degradation of the nucleic acid to be analyzed by an exonuclease. The adapter structure is then recited. However, the claim does not identify what is the nucleic acid that is to be analyzed.
The claim is totally indefinite because the specification does not clearly teach how the nucleic acid-adapter molecule complex inhibits the degradation of the nucleic acid to be analyzed.
Figure 7 is representative the nucleic acid-adapter molecule (reproduced below):
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According to the specification, the “adapter” portion comprises element 114 which is discussed by the specification that inhibits the exonuclease degradation (see section [0052], “streptavidin (the diameter is about 5 nm) can be used as the degradation inhibition portion 114. When streptavidin binds to a terminal, biotin binds to the terminal”). Therefore, the nucleic acid to be analyzed (301B) is not protected from the exonuclease at all. As well, the nucleic acid to be analyzed of the above structure also appears to be the same strand (301A) that comprises the exonuclease inhibitor 114 because this strand comprises a primer binding and DNA polymerase binding site (regions 303 and 302, respectively, see sections [0098]).
Therefore, it is completely unclear just exactly how the nucleic acid-adapter molecule results in the inhibition of the nucleic acid to be analyzed and just exactly what the adapter structure is.
Claims 11-16 are indefinite by way of their dependencies on claim 10.
Claim 13 is indefinite because the claim does not contain an active step of providing a primer. Claim 13 recites that a “single-stranded nucleic acid region … includes a primer binding portion to which a primer is hybridizable” without actively requiring that the primer is actively provided. This is notwithstanding the phrase, “the DNA polymerase … synthesizes the complementary strand from the primer hybridized to the primer binding portion” because this can be construed as an intended usage, not an active step.
Claim 14 recites the phrase, “the single-stranded nucleic acid region including the molecular motor binding portion includes plural sets including the molecular motor binding portions and primer binding portions”.
This is indefinite because the single-stranded nucleic acid region is recited as having a single molecular binding portion (see parent claim 12) and there isn’t a sufficient antecedent basis for the primer binding portion (or portions).
Claim 15 recites the phrase, “the primer binding portion.”
There is an insufficient antecedent basis for the limitation.
Claim 16 is indefinite for reciting the phrase, “complementary strand from the primer hybridized to the primer binding portion.”
There is an insufficient antecedent basis for the limitation.
Claims 11-16 are also indefinite by way of their dependency on claim 10.
Claim Rejections - 35 USC § 102
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.
Claim 8 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Turner et al. (WO 2010/117470 A2, published October 2010).
With regard to claim 8, Turner et al. teach a method of sequencing a nucleic acid molecule (thus “analyzing”), comprising the steps of:
synthesizing a complementary strand of a nucleic acid to be analyzed by DNA polymerase in a solution including a nucleic acid to be analyzed, DNA polymerase, nucleotide as a substrate of DNA polymerase, and exonuclease and determining a sequence of a base in response to the synthesis of one base by the DNA polymerase (“invention utilizes a polymerase/exonuclease pair to push and then pull back a DNA strand in the nanopore. In some cases, two separate enzymes can be used… adding nucleotides and making use of the polymerization process to push/pull the dna through the nanopore for detection … allowing exonuclease activity to kick in and push/pull the dna in the opposite direction of the polymerase activity”, section [00191]); and
step of degrading the complementary strand synthesized by DNA polymerase with exonuclease (when exonuclease pulls the DNA in the opposite direction, the synthesized DNA is cleaved).
As well, in an alternative embodiment, the artisans also teach that the polymerase and exonuclease combination can be utilized to polymerize and then cleave the synthesized strand bases to pass through the nanopore, allowing for multiples reads on the same strand of DNA:
“if the desire is to read a cleaved moiety, it has been suggested to use an exonuclease to cleave off a base, which then passes through the pore and detected. The invention disclosed here uses a polymerase/exonuclease pair to first polymerize, and use a modified cleaved phosphate group as a detection moiety. Then after one or more bases, activate exonuclease activity and detect the cleaved base … incorporating both polymerase and exonuclease activity can improve overall sequencing accuracy” (section [00191])
Therefore, the invention as claimed is anticipated by Turner et al.
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 10-16 are rejected under 35 U.S.C. 103 as being unpatentable over Turner et al. (WO 2010/117470 A2, published October 2010) in view of Akahori et al. (GB 2603061 A1, published July 27, 2022, priority September 18, 2019).
Teachings of Turner et al. have already been discussed above.
Turner et al. do not teach that the nucleic acid to be sequenced is complexed to form a nucleic acid-adapter molecule, wherein the adaptor molecule directly or indirectly binds to at least one portion of the nucleic acid to be analyzed such that degradation by an exonuclease is inhibited (claim 10).
Turner et al. do not teach that the adapter comprises a double-stranded nucleic acid region having the configuration recited in claim 11, having a molecular motor binding portion to which a DNA polymerase is bindable (claim 12), having a primer binding portion (claim 13), a spacer (claim 15), molecular motor detachment portion and movement of the nucleic acid-adapter molecule for separating the detachment of the polymerase (claim 16).
Akahori et al. teach a similar means of sequencing a nucleic acid molecule via a nanopore (see Figure 1), wherein the artisans teach an adapter (113) that is directly attached to the nucleic acid to be sequenced (112), said adapter conferring a resistance to exonuclease degradation (“adapter molecule 111 includes a fall-off prevention portion 113 at an end opposite to an end bound1 to the biomolecule 109”, section [0063]).
With regard to claim 11-13 and 15, Akahori et al. teach an adapter comprising the configuration as claimed in claim 11 (see below):
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As seen, the adapter comprises a double-stranded nucleic acid region, and a pair of single-stranded nucleic acid region different from one end portion and consists of base sequence non-complementary to each other (301A and 310B), and degradation inhibition portion is provided on one of the pair of single-stranded nucleic acid regions (see element 113), and this region is not introduced into the second tank (see Fig. 14A and B) similar to the way in which the DNA being sequenced does not result in its 3’ end traveling through the nanopore (into a second chamber). As well, the adapter comprises a molecular binding portion to which DNA polymerase is bindable (see region 302 above, and polymerase 130 being bound to that region in Fig. 14A), meeting the limitation of claim 12. As well, the single-stranded region includes a primer binding portion (region 303 of above), and primer binds to this region (see element 131 of Fig. 14A), meeting the limitation of claim 13. As well, a spacer region is provided between the molecular binding portion and the primer binding portion (element 304 of above), meeting the limitation of claim 15.
Akahori et al. also teach that the adapter comprises the same configuration as claimed in instant claim 16 (see sections [0035] and [0036]).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Turner et al. with the teachings of Akahori et al., thereby arriving at the invention as claimed for the following reasons.
As discussed above, Turner et al. teach a method of sequencing a nucleic acid via a nanopore utilizing a combination of a polymerase and an exonuclease.
The sequencing mechanism by which Turner et al. employ, pulls the nucleic acid sequence from the first chamber (where the nucleic acid and the polymerase is) through a nanopore in to a second chamber, wherein when the polymerase binds to the nucleic acid and polymerization ensues, the nucleic acid is pulled from the second chamber back into the first chamber via the nanopore.
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And while Turner et al. do not explicitly teach that the nucleic acid to be sequenced should be contacted with an adapter, one of ordinary skill in the art would have motivated to combine the teachings of Akahori et al. in using an adapter of the disclosure so as to initiate the sequencing reaction in a predicable manner in pulling down the nucleic acid sequence through the nanopore (into a second chamber) and push the bound polymerase up and adjacent to the primer (through the spacer region), wherein upon binding, the polymerase polymerizes and initiates the sequencing reaction:
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One of ordinary skill in the art would have had a reasonable expectation of success at combing the teachings of Turner et al. with the teachings of Akahori et al. because both methods are directed toward sequencing a nucleic acid molecule via a nanopore structure, wherein the sequencing means first “pulls down” the nucleic acid molecule into the second chamber (i.e., bottom) through the nanopore and the sequencing reaction commences when the polymerase polymerizes the nucleic acid on the upper chamber, thereby “pulling up” the nucleic acid sequence through the nanopore. Adding an adapter structure to the nucleic acid sequence in the method of Turner et al. would not have altered the way in which the method of sequencing operated, allowing for the combination to benefit from the controlled initiation of the sequencing reaction as taught by Akahori et al.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Claim 9 is free of prior art.
While Turner et al. teach that a polymerase and exonuclease is utilized the above-discussed method of sequencing, the mechanism by which exonuclease is employed is structurally different from that of claim 9.
This is because the exonuclease reaction suggested by Turner et al. is implied to be at the bottom chamber (i.e. second chamber) of the sequencing system and the polymerase is located on the top chamber (i.e., first chamber):
“adding and making use of the polymerization process to push/pull the dna through the nanopore for detection … allowing exonuclease activity to kick in and push/pull the dna in the opposite direction of the polymerase activity” (section [00191]).
When an exonuclease acts on a DNA molecule through a nanopore, the movement of the DNA is directed toward the chamber in which exonuclease is.
Because the polymerase activity in Turner et al.’s system pulls the nucleic acid up into the chamber in which the DNA polymerase is placed, in order for the exonuclease to direct the DNA in an opposite direction of the polymerase, the exonuclease must be located on the opposite side of the DNA polymerase (see Figure 10).
Because claim 9 requires that both the exonuclease and DNA polymerase be located in the same chamber (i.e., first liquid tank), there is no motivation to arrive at a system employed in the method of claim 9.
The embodiment of claim 9 is represented by instant Figures 4-6, and differs from the teachings of Turner et al.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 February 9, 2026
/YJK/
1 the “fall-off prevention” portion 113 is further described as streptavidin (see section [0073], Akahori), which is the same agent described in the instant specification as providing degradation protection (see instant specification, “streptavidin (the diameter is about 5 nm) can be used as the degradation inhibition portion 114”, section [0052]).