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 I (claims 1-6 and 22-32) in the reply filed on 01/23/2026 is acknowledged.
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 1-6, 22-32 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 1 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps are: the preamble states a method of linearizing a plurality of immobilized double-stranded polynucleotide but none of the steps of the method actually perform said reaction. Without any active, positive steps delimiting how the method is actually practiced, it is unclear how the method of claim 1 is performed. While minute details are not required in method claims, at least the basic steps must be recited in a positive, active fashion (See ex parte Erich, 3 UsPQ2dl011, p. 1011 (Bd. Pat, Applicant. Int. 1986). Clarification is required.
Claim 1 is vague and indefinite because it is unclear what exactly is the primer sequence for the “P17' primer sequence”. No definition for the P17' primer sequence is present in the claim. Additionally, claim 1 must specify that the P17' primer sequence is located at the 5' end of the second strand. This is essential as a different position of the P17' primer sequence would lead to a non-working construct.
Note that although the claims are interpreted in light of the specification,
limitations from the specification are not read into the claims. Also see In re Van Geuns,
988 F.2d 1181,26 USPQ2d 1057 (Fed. Cir. 1993). Also see, In re Zetz, 13 USPQ2d
1320,1322. "An essential purpose of patent examination is to fashion claims that are
precise, clear, correct and unambiguous." .
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 1-6 and 22-32 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 17, 29-31, 33, 35 of copending Application No. 18568600 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they both claim a method of linearizing a plurality of immobilized double-stranded polynucleotides comprising identical steps. And using composition comprising a periodate salt and an ionic liquid additive; wherein the ionic liquid additive comprises 1-benzyl-3-methylimidazolium chloride ([Bzmim]Cl); wherein the molar ratio of [Bzmim]Cl to the periodate salt is from about 1:1 to about 100:1, from about 10:1 to about 50:1, or about 30:1. (see reference application claims 29-31, 33, 35). The reference application teaches that the cleavage site of each second strand comprises one or more diol linkers. In some embodiments, the diol linker comprises a structure of Formula (I) or (Ia) [0014].
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-6 and 22-32 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 18, 30-31 and 33 of copending Application No. 18568756 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they both claim a method of linearizing a plurality of immobilized double-stranded polynucleotides comprising identical steps. And using composition comprising a periodate salt and an ionic liquid additive; wherein the ionic liquid additive comprises 1-benzyl-3-methylimidazolium chloride ([Bzmim]Cl); wherein the molar ratio of [Bzmim]Cl to the periodate salt is from about 1:1 to about 100:1, from about 10:1 to about 50:1, or about 30:1. (see reference application claims 30-31 and 33). The reference application teaches that the cleavage site of each second strand comprises one or more diol linkers. In some embodiments, the diol linker comprises a structure of Formula (I) or (Ia) [0017].
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
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(s) 1, 3-6 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wu et al. US 2019/0352327.
Wu et al. teaches methods of chemical linearization of clusters of double-stranded polynucleotides immobilized on a solid support for generating a template for sequencing. Each double-stranded polynucleotide comprises a first strand and a second strand. The first strand is generated by extending a first extension primer immobilized to the solid support and the second strand is generated by extending a second extension primer immobilized to the solid support. Each of the first and the second strand comprises a cleavage site… In some embodiments the second strand comprises a cleavage site that include a diol linker that is capable of being cleaved by a periodate, for example, NaIO4. [0050]; [0131].
Wu et al. teaches the diol linker has a structure identical to the instant formula (I) and (Ia) (page 7).
Wu et al. teaches the methods include cleaving one or more second strands at the second cleavage site, thereby generating one or more cleaved second nucleic acids and cleaved immobilized second strands, and removing the cleaved second nucleic acids from the solid support. In such methods, the immobilized derivative first strands remain on the solid support following removal of the cleaved second nucleic acids from the solid support, and remain hybridized to the cleaved immobilized second strands [0014]; [0136].
Wu et al. teaches wherein the cleavable site comprises at least two diol linkers (see page 9, col 1 where the primer sequence SEQ ID NO.6 comprises 3 diol linkers represented by YYY).
Claim(s) 1, 3-6 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu et al. US 2009/0118128 (US version of WO2007/010251) both cited in IDS filed 07/06/2023).
Liu et al teaches a method of generating a template for a nucleic acid sequencing reaction comprising, (i) providing a solid supported polyacrylamide hydrogel having attached thereto one or more double-stranded nucleic acid molecules, wherein both strands of the double-stranded nucleic acid molecule are attached to the polyacrylamide hydrogel at the 5' end, (ii) cleaving one or both strands of the double-stranded nucleic acid molecule, and (iii) subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the polyacrylamide hydrogel, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction. (see [0015] and claim 1).
In FIG. 1., Liu et al. discloses a schematic illustration of cluster formation by solid-phase PCR and subsequent linearisation and annealing of a sequencing primer. The starting material in step (a) is a solid support grafted with a mixture of amplification primers, one of which comprises a cleavage site. The primers are covalently attached to the solid support at the 5' end. A substrate molecule to be amplified is also applied to the solid support, either by hybridisation to one of the immobilised primers or by direct covalent attachment to the support at the 5' end. (this is viewed as the instant plurality of immobilized double-stranded, wherein each double-stranded polynucleotides comprises a first strand and a second strand, the first strand and the second strand are immobilized to the solid support at their 5' ends). FIG. 1(b) schematically illustrates the "bridged" amplification products resulting from solid phase amplification. For simplicity only a small number of bridged products are shown. The amplification products are then "linearised" by cleavage at the cleavage sites derived from the amplification primers (FIG. 1(c)). Liu et al. discloses the products of the cleavage reaction may then be subjected to denaturing conditions, resulting in removal of the portions of the cleaved strands which are no longer covalently attached to the solid support (FIG. 1(d)). (this is viewed as the cleaved second polynucleotides, and instant claim 3).[0028]
Liu et al. discloses the method wherein one strand of the double-stranded nucleic acid molecule comprises a diol linkage and cleaving this strand at the diol linkage by treatment with periodate. (see [0052- 0058], claims 1, 19-20).
Liu et al. discloses the primers are typically oligonucleotide molecules having the following structures: Forward primer: A-L-S1 Reverse primer: A-L-S2. [0128]; [0132]. Modifications required to enable subsequent cleavage of the bridged amplification products may be advantageously included in one or both amplification primers. The modifications which enable cleavage may form part of the linker region L or one or both of sequences S1 or S2. By way of example, the amplification primers may be modified to include inter alia diol linkages [0147] (this is viewed to be inclusive of the primer comprising a cleavage site having one or more diol linkers and instant claim 4).
Liu et al. discloses structure of the "diol" linker incorporated into the cleavable primer identical to instant formula (I) and (Ia) (see [0212]; [0235-0236], [0259], [0263], [0267]).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEZIA RILEY whose telephone number is (571)272-0786. The examiner can normally be reached 7:30-6:00pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JEZIA RILEY/ Primary Examiner, Art Unit 1681 20 February 2026