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 .
Notice of New Examiner
This case has been transferred to a new examiner for continued examination. Any further communications regarding this case may be directed to the contact information included in the conclusion of this office action.
Election/Restriction
Applicant’s election with traverse of Group I (Claims 1-12) in the reply filed on 05/11/2026 is acknowledged. The traversal is on the ground(s) that Group II (claims 13-15) require the peptide of claim 1.
Applicant’s election of species without traverse of SEQ ID NO: 1 in the reply filed on 05/11/2026 is acknowledged.
Upon reevaluation, all groups and species have been rejoined.
Claim Status
Claims 1-17 are pending. No claims are canceled. Claims 1-17 are herein examined.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 05/07/2026 and 01/18/2018 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure is being considered by the examiner.
Claim Objections
Claim 16 is objected to because of the following informalities: claim 16 recites two part “(f)” components. For the purposes of examination “(f) a set of…” will be interpreted as “(h) a set of …”. Appropriate correction is required.
Claims 16 and 17 are objected to because of the following informalities: the recitation of nucleoside oligophosphates contains a missing character:
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For the purposes of examination, it will be interpreted as nucleoside-5’-oligophosphates. Appropriate correction is required.
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.
Claim 16 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 16 is rejected as indefinite because it recites “…wherein each of the polymer-tagged nucleoside-[5’]-oligophosphates is the nucleoside-[5’]-oligophosphate” (emphasis added). The phrase “the nucleoside” lacks antecedent basis and it is unclear what “the nucleoside” is referring to, rendering the metes and bounds of the claim unclear. For the purposes of examination this limitation will be interpreted as “wherein each of the polymer-tagged… is a nucleoside-5’-oligophoshate”.
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)(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.
Claim(s) 1, 2, and 13-15 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by US20240167086A1 (hereafter “Crisalli”) which has an earliest effective filing date of 06-17-2021 (see instant PTO-892).
The applied reference has a common assignee with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Instant claims 1 and 2 recite a polypeptide comprising a variant narrow channel alpha-hemolysin subunit comprising at least 85% identity to SEQ ID NO: 4. Claims 13-14 recite a narrow channel alpha-hemolysin nanopore comprising at least 6 variant narrow channel alpha-hemolysin subunits of claim 1. Claim 15 further limits that the nanopore is a 6:1 nanopore wherein one subunit is attached to a DNA polymerase.
Regarding claims 1 and 2, Crisalli teaches SEQ ID NO: 2, which comprises all of instant SEQ ID NO: 4 (see below) [0114]. Because the substitutions at specific amino acid positions recited in Claim 1 correspond to the residues of SEQ ID NO: 1, the claim will be interpreted as only requiring the following substitutions if SEQ ID NO: 1 is selected in part (a) of claim 1: a D127G and a D128K substitution relative to SEQ ID NO: 1, as well as at least of one i) an amino acid at a position corresponding to E111 of SEQ ID NO: 1 that has a sidechain that is longer than the sidechain of asparagine, ii) an amino acid at a position corresponding to K147 of SEQ ID NO: 1 that has a sidechain that is longer than the sidechain of asparagine, and/or iii) an amino acid at a position corresponding to M113 of SEQ ID NO: 1 that has a sidechain that is longer than that of alanine.
Regarding claims 13-15, Crisalli teaches a 6:1 alpha-hemolysin nanopore, formed from 6 alpha-hemolysin subunits comprising SEQ ID NO: 2 and one alpha-hemolysin subunit that is attached to a DNA polymerase ([0114]; pg. 18). Regarding claim 14, the limitation “comprising a D127G and a D128K substitution relative to SEQ ID NO: 1” is interpreted as only being required if the polypeptide selected in part (a) of Claim 1 is SEQ ID NO: 1. Therefore, the nanopore taught by Crisalli reads on claims 13-15.
Regarding claims 16 and 17, Crisalli teaches a system for performing nucleic acid sequencing-by-synthesis ([0088]; Figs. 1 and 2), comprising:
(a) a chip (Fig. 2 part 200; [0096]) comprising a plurality of sensing electrodes (Fig. 1, parts 106 and 107; [0094] lines 1-3),
(b) an electrochemically resistive barrier ([0090], line two; Fig. 1 part 101) that has a cis and trans side (Fig. 1, parts 102 and 103; [0092]) and is disposed on the surface of the chip (Fig. 2, parts 240, 220),
(c) a first electrolyte solution on the cis side of the barrier (Fig. 1 part 102; [0092] lines 1-5),
(d) second electrolyte solution on the trans side of the barrier (Fig. 1, part 103; [0092], lines 1-5),
(e) a plurality (Fig. 2, parts 240 and 250; [0096]) of narrow channel alpha hemolysin nanopores which comprise SEQ ID NO: 2 (which is at least 75% identity to instant SEQ ID NO: 4) ([0114]) that are disposed in the barrier (Fig. 1, parts 104 and 101) and permit ion exchange between the electrolyte solutions ([0093], last three lines) and the sensing electrodes can detect electrical characteristics of the barrier such as resistance, capacitance, voltage, and ionic current flow ([0095]),
(f) a processor (Fig. 3 part 324, [0100] last three lines) in electronic communication with the sensing electrodes (Fig. 3, part 322) and can analyze sequencing data to determine sequences of polymer molecules ([0100], last five lines), which necessarily requires that it can record the characteristics of electrical current flowing through the nanopore,
(g) a nucleic acid (Fig. 4, part 410; [0107]) polymerase (Fig. 4, part 409) associated with the nanopore (Fig. 4, parts 409 and 404) that can catalyze incorporation of the polymer-tagged nucleotides into an amplicon of the template ([0107], middle of paragraph) in the first electrolyte solution (Fig. 4, parts 402, 409, 410, and 404), and
(h) polymer tagged nucleoside polyphosphates are in the first electrolyte solution (Fig. 4, part 411; [0107]) that including deoxyadenosine-5′-oliogophosphate (dA5OP), deoxycytidine-5′-oliogophosphate (dC5OP), deoxyguanosine-5′-oliogophosphate (dG5OP), a deoxythymidine-5′-oliogophosphate (dT5OP) and/or a deoxyuridine-5′-oliogophosphate (dU5OP) (pg. 19, claim 5).
Regarding claim 17, Crisalli further teaches that using the system described above, the tagged nucleoside-5’-oligophosphates move through the nanopore channel after complexing with the polymerase, which generates a unique signal based on how the specific tagged nucleoside-5’-oligophosphate affects the ionic flow of the nanopore ([0107], middle of paragraph). Crisalli further teaches that the changes in current flow can be detected via a sensing electrode and recorded on a computer system (Fig. 3), and used to determine the sequence of complementary nucleic acid generated at that electrode ([0107]).
Thus, instant claims 1, 2, 13-17 are anticipated.
SEQ ID NO: 2 of Crisalli:
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMGKKVFYSFIDDKKHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKNYASTLTYGFNGNVTGGKGGGIGGLIGANVSIGATLNYKQPDFKTILESPTDKKVGWKVIFNNMVNQNWGPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTNGLSAWSHPQFEK
Instant SEQ ID NO: 4:
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMGKKVFYSFIDDKKHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKNYASTLTYGFNGNVTGGKGGGIGGLIGANVSIGATLNYKQPDFKTILESPTDKKVGWKVIFNNMVNQNWGPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 16 and 17 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 15 and 16 of copending Application No. 18041348 (hereafter “reference application”) in view of US20240167086A1 (hereafter “Crisalli”) which has an earliest effective filing date of 06-17-2021 (see instant PTO-892).
Regarding instant claim 16, the reference application claim 15 teaches a system for performing nucleic acid sequencing-by-synthesis (SBS) comprising:
a chip comprising a plurality of sensing electrodes;
an electrochemically resistive barrier disposed on a surface of the chip, wherein the barrier has a cis side and a trans side;
a first electrolyte solution on the cis side of the barrier;
a second electrolyte solution on the trans side of the barrier;
a plurality of nanopores comprising a channel having sufficient negatively charged moieties to substantially repel a template and/or primer nucleic acid, wherein the nanopores are disposed in the barrier such that the channel permits ion exchange between the first electrolyte solution and the second electrolyte solution, and wherein at least a portion of the nanopores are close enough to one of the sensing electrodes that the sensing electrode can detect at least one characteristic of an electrical current flowing through the channel of the nanopore;
a computer system in electronic communication with the sensing electrodes, wherein the computing system is adapted to record the characteristic of the electrical current flowing through the nanopore that is detected by the sensing electrode;
a nucleic acid polymerase associated with the nanopore on the cis side of the barrier, wherein the nucleic acid polymerase is capable of catalyzing a template-dependent nucleic acid amplification reaction in the first electrolyte solution; and
a set of nuclcoside-5'-oligophosphatcs disposed in the first electrolyte solution, the set including at least a polymer-tagged adenosine nucleoside-5'-oligophosphate, a polymer-tagged guanine nucleoside-5'-oligophosphate, a polymer-tagged cytosine nucleoside-5'-oligophosphate, and either a polymer-tagged thymidine nucleoside-5'-oligophosphate or a polymer-tagged uracil nucleoside-5'- oligophosphate.
Regarding instant claim 17, claim 16 of the reference application teaches a method of sequencing a template nucleic acid comprising using the system recited in claim 15 to a) detect changes in current flow through the nanopore caused by the polymer tags using a sensing electrode, b) record the change on a computer system, and c) correlate the change with a specific tagged nucleoside-5’-oligophosphate to generate the sequence of the commentary nucleic acid generated at that electrode.
Thus, the only difference between instant claims 16 and 17 and reference application claims 15 and 16, respectively, is that the reference application recites using generic nanopores in the SBS system, while the instant claims recite specifically using narrow channel alpha hemolysin nanopores.
The teachings of Crisalli are above.
It would be obvious to one of ordinary skill in the art to modify the SBS system and method of sequencing a template nucleic acid of the reference application with narrow channel alpha hemolysin nanopores comprising SEQ ID NO: 2 of Crisalli. In other words, instant claims 16 and 17 are an obvious embodiment of the claims 15 and 16 recited in the reference application. One of ordinary skill in the art would be motivated to use narrow channel alpha hemolysin nanopores comprising SEQ ID NO: 2 as the nanopores in the SBS system of the reference application because Crisalli explicitly teaches implementing the nanopore into an SBS system. For this reason, there would also be a reasonable expectation of success.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 17 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 9 of copending Application No. 18/542,500 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 9 of the reference application recites a method of sequencing a DNA molecule comprising:
(a1) a sensing electrode; (a2) a nanopore positioned in proximity to the sensing electrode such that the sensing electrode can detect changes in at least one electrical characteristic of the nanopore; (a3) a DNA-dependent DNA polymerase linked to the nanopore; and (a4) a sequencing solution comprising the set of nucleoside-5’-oligophosphates (N5OPs) including adeoxyadenosine-5′-oliogophosphate (dA5OP), a deoxycytidine-5′-oliogophosphate (dC5OP), a deoxyguanosine-5′-oliogophosphate (dG5OP), a deoxythymidine-5′-oliogophosphate (dT5OP), and/or a deoxyuridine-5′-oliogophosphate (dU5OP) (b) incorporating an N5OP of the set of N5OPs into an amplicon of the DNA molecule in a template-dependent amplification reaction mediated by the DNA-dependent DNA polymerase using the DNA molecule as a template, wherein the nanopore-detectable tag construct of the N5OP incorporated into the amplicon inserts into the nanopore during incorporation, thereby changing the electrical characteristic of the nanopore detected by the sensing electrode; and (c) correlating the change in the electrical characteristic of the nanopore to the identity of the N5OP incorporated into the amplicon; and (d) repeating (a)-(c) for each N5OP incorporated into the amplicon, thereby sequencing the DNA molecule.
Thus, the difference between instant claim 17 and claim 9 of the reference application is that claim 9 recites a generic nanopore in (a2) while the instant claim requires a narrow channel alpha hemolysin nanopore.
However, the specification of the reference application teaches that the nanopores used in the SBS system can be narrow channel alpha hemolysin nanopores comprised of subunits comprising SEQ ID NO: 2 ([0114]), which is at least 75% identity to instant SEQ ID NO: 4.
Thus, it would be obvious for one of ordinary skill in the art to modify the nanopore in the method of sequencing a DNA molecule of the reference application with a narrow channel alpha hemolysin nanopore specifically comprised of subunit polypeptides comprising SEQ ID NO: 2 of the reference application. In other words, instant claim 16 is an obvious embodiment of reference application claim 15. The species of narrow channel alpha hemolysin nanopore used for SBS, as recited in instant claim 16, is rendered obvious over the genus of nanopores used for SBS recited in claim 15 of the instant application, in view of the teaching of the narrow channel alpha hemolysin nanopore in the reference application specification.
The MPEP § 804 (II)(B) teaches that: “In construing the claims of the reference patent or application, a determination is made as to whether a portion of the specification, including the drawings and claims, is directed to subject matter that is within the scope of a reference claim. For example, assume that the claim in a reference patent is directed to a genus of compounds, and the application being examined is directed to a species within the reference patent genus. If the reference patent discloses several species within the scope of the reference genus claim, that portion of the disclosure should be analyzed to properly construe the reference patent claim and determine whether it anticipates or renders obvious the claim in the application being examined. Because that portion of the disclosure of the reference patent is an embodiment of the reference patent claim, it may be helpful in determining the full scope and obvious variations of the reference patent claim” (emphasis added).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Allowable Subject Matter
Claims 3-10 are free of the art because in the prior art search there were no results found for a sequence with 75% identity to SEQ ID NO: 1, with D127G and D128K substitutions relative to SEQ ID NO: 1 or with a) E111 substitutions to an amino acid that has a sidechain longer than asparagine, b) K147 substitutions to an amino acid that has a side chain that is longer than asparagine, or c) M113 substitutions to an amino acid that is longer than alanine.
Claim 11 is free of the art. In the prior art search, there were no results found for a sequence with 75% identity to SEQ ID NOs: 1-8 that also comprised the necessary substitutions recited in 11(a)-(h). Therefore, Claim 12, which depends from claim 11 is also free of the art.
From the search conducted, the formation of narrow channel alpha hemolysin nanopores by mutation of alpha hemolysin subunit polypeptides to comprise Glycine at position 127 and lysine at position 128 is novel. Where sequences of alpha hemolysin subunit polypeptides already comprise one or both of these amino acids at these respective positions, such as in SEQ ID NO: 4, it is not obvious to further add the combination of substitutions at positions 111, 147 and 113.
The closest art found is:
US20180002750A1 (see instant PTO-892; hereafter “Ambroso”) which teaches alpha hemolysin variants comprising the following substitutions of the wild-type alpha hemolysin: E111S, M113S, K147S, and D127G, and D128G. Ambroso does not teach or suggest an alpha-hemolysin subunit variant comprising both Glycine at residue 127 and lysine at residue 128.
US20240167086A1 (see instant PTO-892; hereafter “Crisalli”) which has an earliest effective filing date of 06-17-2021. Crisalli teaches SEQ ID NO: 2, which comprises instant SEQ ID NO: 4 but does not have a glutamic acid at position 111, lysine at position 147, or methionine at position 113. Furthermore, the combination of these substitutions over the prior art is nonobvious.
Stoddart (Nucleobase recognition in ssDNA at the central constriction of the αhemolysin pore, 2010, Nano. Lett., pgs. 3633–3637; see instant PTO-892) teaches substitutions at the 113 position (abstract) of alpha-hemolysin subunits in order to enhance DNA sequencing via mutant alpha-hemolysin nanopores. However, Stoddart teaches away from a methionine substitution at this position because was not able to discriminate between all four bases (Fig. 3A).
It would not be obvious to combine Crisalli and Stoddart to arrive at the polypeptide of instant claim 11(d) because there is no teaching, suggestion, or motivation in either source to modify all constriction site residues of alpha-hemolysin subunits, namely positions 111, 113, and 147, particularly to the glutamic acid, methionine, and lysine, respectively. Furthermore, there is no evidence in Stoddart or Crisalli that narrowing the constriction site of the nanopore by mutation for nanopore DNA sequencing, as taught by Stoddart, would have a reasonable expectation of success when applied to nanopore SBS, which requires the passage of bulkier tagged nucleotides.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHELLE C BUCCINI whose telephone number is (571)272-1352. The examiner can normally be reached M-F 7:30-5 EST.
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/MICHELLE CALLAHAN BUCCINI/Examiner, Art Unit 1675
/JEFFREY STUCKER/Supervisory Patent Examiner, Art Unit 1675
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