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 .
This application is a domestic application, filed 15 Dec 2023; and claims benefit as a CON of PCT/EP2022/066263, filed 15 June 2022, which claims benefit of provisional application 63/202,626, filed 17 June 2021.
Claims 1-9 are pending in the current application. Claims 8-9, drawn to non-elected inventions, are withdrawn. Claims 1-7 are examined on the merits herein.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-7, in the reply filed on 26 May 2026 is acknowledged.
Claims 8-9 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 26 May 2026.
Applicant’s election of species of base-modified nucleoside-5’-oligophosphate of formula 1, in which R1 is
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, R2 is OH, R3 is H, and R4 is H, in the reply filed on 26 May 2026 is acknowledged.
During a telephone conversation with Kristen Walker on 07 July 2026 a provisional election of species was made regarding the PCM group to select the species of compound wherein the PCM group has formula 2a. Affirmation of this election must be made by applicant in replying to this Office action.
Search and examination has expanded to include the compound wherein R1 is uridine or 7-deazaadenosine, corresponding to the 2nd and 10th listed groups R1, and the compound wherein one of R4 is a nanopore-detectable tag construct.
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 1-7 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 recites a Formula 1 that appears as “
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” and a group R1 that appears as “
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”.
Claim 2 recites a Formula 2 that appear as “
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”.
Claim 4 recites a similar black box for the Formulas 2a through 2h.
These recitations render the claim indefinite because it is unclear what formula is required. Claim 3 depends from claim 2, and incorporates the limitations of claims 1 and 2, and is indefinite for the same reason. Claims 5-7 depend from claim 1 and incorporate the limitations therein, and are indefinite for the same reason. For the purpose of examination, the claims have been interpreted based on formulas recited at pages 3-5 of the specification.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 1-4 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hobbs Jr. et al. (US 5,047,519, issued 10 Sep 1991, cited in PTO-892).
Hobbs Jr. et al. discloses alkynylamino-nucleotides and labeled alkynylamino-nucleotides useful, for example, as chain terminating substrates for DNA sequencing (abstract). These compounds are of general formula
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where Nuc is a heterocyclic base attached to a sugar or sugar-like moiety (column 7, line 25 to column 8, line 10). Hobbs Jr. et al. discloses the working example 8 of 5-(3-amino-1-propynyl)-2'-deoxycytidine 5'-triphosphate (54) (column 47, line 10 to column 48, line 35), or the elected species of compound of formula 1, where R1 is the 5-subtituted cytidine, R2 is OH, R3 is H, R4 is H, a is 3, and the group PCM is formula 2a where b is 1. Hobbs Jr. et al. discloses the charged form of the compound where the amino group is protonated (column 14, line 55), or the formula 2a where all three of R5 are H.
Regarding claim 1, Hobbs Jr. et al. does not specifically describe the amino group in terms of “having a net-positive charge at 25° C. when in a reference solution buffered at pH 7-8 and comprising 450 mM potassium acetate”. MPEP 2112.01 especially at I. citing In re Best, 562 F.2d 1252, 195 USPQ 430 (C.C.P.A. 1977) and In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990) discusses the support of rejections wherein the prior art discloses subject matter which there is reason to believe inherently includes functions that are newly recited or is identical to a product instantly claimed. In such a situation the burden is shifted to the applicants to show the products of the applicant and the prior art are not the same or that the prior art products do not necessarily possess the characteristics of the claimed product. In this case Hobbs Jr. et al. discloses the same compound of 5-(3-amino-1-propynyl)-2'-deoxycytidine 5'-triphosphate and describes it in protonated or cationic form, thus there is reason to believe the prior art discloses subject matter that is identical to the product instantly claimed.
Hobbs Jr. et al. further discloses embodiments of the compound wherein the base is dideoxyuridine (example 2 at column 32) and dideoxy-7-deazaadenosine (example 4 at column 38), corresponding to the 2nd and 10th listed groups R1, and wherein R2 and R3 are both H.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-6 are rejected under 35 U.S.C. 103 as being unpatentable over Hobbs Jr. et al. (US 5,047,519, issued 10 Sep 1991, cited in PTO-892) in view of Jett et al. (US 5,405,747, issued 11 April 1995, cited in PTO-892).
Hobbs Jr. et al. teaches as above. Hobbs Jr. et al. further teaches it is desired to prepare a set of four alkynylamino nucleosides as the 5’-triphosphates corresponding to the four nucleobases in order to prepare fluorescently-labeled DNA (column 24, line 15 to column 26, line 65).
Hobbs Jr. et al. does not specifically disclose a set of nucleoside-5’-oligophosphates (claim 5). Hobbs Jr. et al. does not specifically disclose the set wherein each of dA5OP, dT5OP or dU5OP, dC5OP, and dG5OP is the bmN5OP of claim 1 (claim 6).
Jett et al. teaches generally the field of DNA and RNA sequencing by the detection of individual nucleotides specifically labeled with fluorescent dyes and excited using electromagnetic radiation (column 1, line 15). Jett et al. teaches the method including enzymatically synthesizing a strand of DNA or RNA complementary to the single fragment of DNA or RNA to be sequenced using bases selected from the group of four bases found in DNA and RNA, a chosen first base being modified in a manner characteristic of that base, while a chosen second base is modified in a manner characteristic of that base; sequentially cleaving the end base from the DNA or RNA strand forming thereby a train of bases, some of which are modified; and adding a fluorescent tag to each modified base appropriate to the modification of that base (column 2, lines 30-45). Jett et al. teaches the example of labeling the different bases AGCT (column 4, line 65 to column 5, line 40).
It would have been obvious to one of ordinary to one of ordinary skill in the art before the effective filing date of the claimed invention to combine Hobbs Jr. et al. in view of Jett et al. in order to obtain a set of nucleoside-5’-oligophosphates and wherein each of the nucleoside-5’-oligophosphates is modified or labeled. One of ordinary skill in the art would have been motivated to combine Hobbs Jr. et al. in view of Jett et al. with a reasonable expectation of success because both Hobbs Jr. et al. and Jett et al. are drawn to the field of DNA and RNA sequencing by the detection of individual nucleotides specifically labeled with fluorescent dyes, Hobbs Jr. et al. suggests motivation to obtain a set of nucleoside-5’-oligophosphates, and Jett et al. suggests the nucleobases AGCT modified in order to be incorporated into the complementary strand of DNA and then labeled, making obvious the set of nucleoside-5’-oligophosphates and wherein each of the nucleoside-5’-oligophosphates is modified or labeled.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Hobbs Jr. et al. (US 5,047,519, issued 10 Sep 1991, cited in PTO-892) in view of Jett et al. (US 5,405,747, issued 11 April 1995, cited in PTO-892) as applied to claims 1-6 above, further in view of Ju et al. (US 2013/0264207, published 10 Oct 2013, provided by Applicant in IDS filed 01 July 2024).
Hobbs Jr. et al. in view of Jett et al. teaches as above.
Hobbs Jr. et al. in view of Jett et al. does not specifically teach the set of N5OPs wherein each of the comprises a nanopore-detectable tag construct (claim 7).
Ju et al. teaches a method of sequencing a single stranded DNA using deoxynucleotide polyphosphate analogues and translocation of tags from incorporated deoxynucleotide polyphosphate analogues through a nanopore (abstract). Ju et al. teaches contacting the single-stranded DNA, wherein the single-stranded DNA is in an electrolyte solution in contact with a nanopore in a membrane and wherein the single-stranded DNA has a primer hybridized to a portion thereof, with a DNA polymerase and four deoxyribonucleotide polyphosphate (dNPP) analogues at least one of which can hybridize with each of an A, T, G, or C nucleotide in the DNA being sequenced under conditions permitting the DNA polymerase to catalyze incorporation of one of the dNPP analogues into the primer if it is complementary to the nucleotide residue of the single-stranded DNA which is immediately 5' to a nucleotide residue of the single-stranded DNA hybridized to the 3' terminal nucleotide residue of the primer, so as to form a DNA extension product, wherein each of the four dNPP analogues has the structure:
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wherein the base is adenine, guanine, cytosine, thymine or uracil, or a derivative of one or more of these bases, and the type of tag on each dNPP analogue is different from the type of tag on each of the other three dNPP analogues (page 1, paragraphs 9-10). In an embodiment, the dNPP analogues for the different nucleobases each have a different tag (page 15, paragraph 188).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine Hobbs Jr. et al. in view of Jett et al. further in view of Ju et al. in order to modify the deoxyribonucleotide polyphosphate analogues taught by Hobbs Jr. et al. in view of Jett et al. with the nanopore-detectable tag of Ju et al. One of ordinary skill in the art would have been motivated to combine Hobbs Jr. et al. in view of Jett et al. further in view of Ju et al. because all of Hobbs Jr. et al., Jett et al., and Ju et al. are drawn to method of sequencing DNA using deoxynucleotide polyphosphate analogues, and Ju et al. teaches an improvement in preparing the DNA, and it would have been obvious to one of ordinary skill in the art to apply this improvement in order to prepare the complementary DNA or RNA fragment taught by Jett et al. Therefore it would have been obvious to obtain the set of deoxyribonucleotide polyphosphate analogues taught by Hobbs Jr. et al. in view of Jett et al. further modified to include a nanopore-detectable tag attached at the end of the polyphosphate chain that is different for each of the nucleobases.
Conclusion
No claim is found to be allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jonathan S Lau whose telephone number is (571)270-3531. The examiner can normally be reached Monday-Friday 9a-5p Eastern.
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/JONATHAN S LAU/ Primary Examiner, Art Unit 1693
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