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 1 and species compound 1608 in FIG. 16C in the reply filed on 01/22/2026 is acknowledged. No prior art was found for the elected species.
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 2-3 and 13 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 2 recites the limitation "the amino acids or amino acid analogs" in line 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 13 recites the limitation "the peptide bond connected to R4…the N-terminal amino acid…" in line 5. There is insufficient antecedent basis for this limitation in the claim.
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.
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.
Claim(s) 1-14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ju et al. US 20150111759 in view of Gremyachinskiy et al. US 20170342485.
Ju et al. discloses a nucleoside 5’-oligophosphate linked to a polymer tag identical to the instant claimed nucleoside compound wherein the tag comprises one or more of ethylene glycol, an amino acid, a carbohydrate, a peptide, a dye, a chemiluminescent compound, a mononucleotide, a dinucleotide, a trinucleotide, a tetranucleotide, a pentanucleotide, a hexanucleotide, an aliphatic acid, an aromatic acid, an alcohol, a thiol group, a cyano group, a nitro group, an alkyl group, an alkenyl group, an alkynyl group, an azido group, or a combination thereof (this is viewed to be inclusive of claims 3 and 10-11), and wherein the tag has a charge which is reverse in sign relative to the charge on the rest of the compound and a composition comprising 4 nucleosides (this is viewed to be inclusive of claim 14) (see page 2). Ju et al. discloses a conductance measurement system comprising a nanopore wherein the interior of the pore has a negative charge and the tag used to identify one of the four nucleotides is a polypeptide with a net positive charge. This system ensures rapid diffusion of the released tags toward the pores while the precursor nucleotides and DNA are repelled. (paragraph [0698]; claims 1,8,25). However, Ju et al. does not refer to a net-positive charge of at least +5 at pH 7.0, and having a charge density of at least 0.1.
But Ju et al. teaches in some instance, the magnitude of the charge on the tag is the same as the magnitude of the charge on the rest of the compound. In an embodiment, the tag has a positive charge and removal of the tag changes the charge of the compound [0237]….optionally, alkaline phosphatase can be used to cleave off all the phosphates to produce a PEG tag with a stronger positive charge [0615]….A different number of charged groups can be used on different tags, depending on the specific nucleotide base. Thus, the cumulative charge of the tag along with its size can be used for base discrimination [0698].
See also Gremyachinskiy et al. teaches “Alternatively, in some embodiments of the tagged multi-nucleotides wherein the tag comprises a polypeptide, the overall charge of the polypeptide is positive, and optionally has an overall charge of between about +10 and +30. In such embodiments, the polypeptide sequence can comprise one or more positively charged amino acid residues, optionally selected from the group consisting of: arginine, lysine, and histidine (this is viewed to be inclusive of claim 2). It is contemplated that in some embodiments the overall charge of the polypeptide can be distributed equally over the length of the tag. In some embodiments, however, the overall charge of the polypeptide tag can be distributed unequally over the length of the polypeptide sequence. Such unequal charge distribution can provide the tag with further distinguishing characteristics under nanopore detection conditions, e.g., either AC or DC potential. Accordingly, in some embodiments the present disclosure provides a tagged multi-nucleotide, wherein the tag comprises a polypeptide and wherein the 25% of the amino acid residues located at the end of the polypeptide tag distal (i.e., further) from the linker have a net charge absolute value greater than the net charge absolute value of the 25% of the amino acid residues located at the end of the polypeptide proximal (i.e., nearer) to the linker. That is, if overall charge is negative, the 25% of the amino acid residues distal from the linker would be more negatively charged than the 25% of the amino acid residues proximal to the linker” [0114]. Additionally, Gremyachinskiy et al. teaches in some embodiments of the linker tag comprises a chemical group selected from the group consisting of: ester, ether, thioether, amine, amide, imide, benzene, benzyl ether, phenol, bis-hydroxyethylbenzene, carbonate, carbamate, squarate, thiazole, thiazolidine, hydrazone, oxime, triazole, dihydropyridazine, phosphodiester, polyethylene glycol (PEG), and combinations thereof [0022] (this is viewed to be inclusive of claims 12-13).
Therefore, one of ordinary skill in the art seeking to solve the stated problem, according to the circumstances, would have been motivated to modify the primary reference in the manner of the claims, without exercising inventive skill, to achieve the expected benefits, optimizations and/or expanded applications as this is well known practice in the art. MPEP states wherein the “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Alter, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). Routine optimization is not considered inventive and no evidence has been presented that the selection of a specific positively-charged segment (PCS) was other than routine, that the products resulting from the optimization have any unexpected properties, or that the results should be considered unexpected in any way as compared to the closest prior art.
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 6 March 2026