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 .
Applicant previously cancels claims 1 and 10. Applicant newly adds claim 18. Claims 2-9 and 11-18 are currently pending and under examination.
Any rejection of record in the previous office actions not addressed herein is withdrawn. New grounds of rejection are presented herein that were not necessitated by applicant’s amendment of the claims since the office action mailed December 12, 2025. Therefore, this action is not final.
Information Disclosure Statement
The Information Disclosure Statement filed March 12, 2026 has been considered.
Claim Rejections - 35 USC § 103
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 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 2-9 and 11-18 are rejected under 35 U.S.C. 103 as being unpatentable over Green R. (United States Patent US 11,299,780 B2, published April 12, 2022, effectively filed July 13, 2017), in view of Amorese et al. (United States Patent US 9,650,628 B2, published May 16, 2017, effectively filed Jan 25, 2013.
Regarding claim 2, Green teaches a composition comprising a plurality of oligonucleotide species, wherein each oligonucleotide in the plurality of oligonucleotide species comprises two strands (Abstract and Column 7, Lines 41-42). Green teaches creating a high efficiency oligonucleotide library (Column 32, Lines 56-63). Green teaches each oligonucleotide in the plurality of oligonucleotide species comprises an overhang at a first end, or some of the oligonucleotides in the plurality of oligonucleotide species comprise an overhang at a first end and some of the oligonucleotides in the plurality of oligonucleotide species comprise no overhang at a first end (Column 13, Lines 3-26). Green teaches the overhang, when present, is capable of hybridizing to a target nucleic acid overhang (Abstract). Green teaches each oligonucleotide species having an overhang has a unique overhang sequence and length (Column 11, Line 44—Column 12, Line 27). Green teaches each oligonucleotide in the plurality of oligonucleotide species comprises, at a second end, two non-complementary strands (Column 31, Lines 18-19, Column 46, Lines 33-35). Green teaches a fluorescent moiety and a 3’ block (Column 1, Lines 46-47) . Green teaches each oligonucleotide in the plurality of oligonucleotide species comprises an oligonucleotide overhang identification sequence specific to no overhang or specific to one or more features of the oligonucleotide overhang, wherein the one or more features comprise length of the overhang (Page 4, [0028], Page 24, [0203], Page 26, [0217]-[0219] and Figs. 25-26).
Regarding claim 3, Green teaches the plurality of oligonucleotide species comprises oligonucleotides having a 5' overhang and oligonucleotides having a 3' overhang (Column 9, Lines 10-20, Column 13, Lines 24-27, Column 14, Lines 46-67 and Column 10, Lines 12-16).
Regarding claim 4, Green teaches the plurality of oligonucleotide species comprises oligonucleotides having a 5' overhang, oligonucleotides having a 3' overhang, and oligonucleotides having no overhang (Column 9, Lines 10-20, Column 13, Lines 24-27, Column 14, Lines 46-67 and Column 10, Lines 12-16).
Regarding claim 5, Green teaches the oligonucleotides in the plurality of oligonucleotide species having overhangs comprising oligonucleotide overhangs having different sequences for a particular overhang length, all possible overhang sequence combinations for a particular overhang length or all possible overhang sequence combinations for each overhang length (Column 11, Line 44—Column 12, Line 27).
Regarding claim 6, Green teaches the oligonucleotide overhang sequences are random (Column 10, Lines 12-23).
Regarding claim 7, Green teaches the oligonucleotide overhang identification sequence is specific to length of the oligonucleotide overhang and is specific to one or more features of the oligonucleotide overhang chosen from (i) a 5' overhang, (ii) a 3' overhang, (iii) a particular sequence, (iv) a combination of (i) and (iii), or (v) a combination of (ii) and (iii) (Column 22, Line 61—Column 23, Line 12).
Regarding claim 8, Green teaches an oligonucleotide species comprises no overhang and comprises an oligonucleotide overhang identification sequence specific to having no overhang (Column 13, Lines 10-27).
Regarding claim 9, Green teaches each of the two non-complementary strands at the second end of the oligonucleotide species comprises a primer binding domain, and one of the non-complementary strands comprises a first primer binding domain, and the other non-complementary strand comprises a second primer binding domain, as well as the first primer binding domain and second primer binding domain are different (Column 17, Lines 7-32 and Column 26, Lines 8-21).
Regarding claim 11, Green teaches each oligonucleotide overhang identification sequence comprises a nucleic acid sequence that is unique for each oligonucleotide comprising an overhang of a particular length or no overhang and a particular 5' or 3' overhang directionality, when an overhang is present (Column 10, Lines 10-40, Column 13, Lines 10-27, Column 22, Line 61—Column 23, Line 12 and Column 14, Lines 7-45).
Regarding claim 12, Green teaches a kit comprising the composition of claim 2 and instructions for using the composition to produce a nucleic acid library (see Claim 2 above, Column 27, Lines 38-44).
Regarding claim 13, Green teaches the kit of claim 12 as discussed above.
Regarding claim 14, Green teaches comprising an agent comprising a phosphoryl transfer activity (Column 45, Lines 13-16).
Regarding claim 15, Green teaches comprising an agent comprising a ligase activity (Column 30, Lines 30-34).
Regarding claim 16, Green teaches comprising an agent comprising a nick-sealing ligase activity (Column 30, Lines 30-34).
Regarding claim 17, Green teaches a strand-displacing polymerase (Column 7, Line56—Column 8, Line 3).
Regarding claim 18, Green teaches each oligonucleotide in the plurality of oligonucleotide species comprises a region adjacent to the overhang or adjacent to a blunt end, wherein the region comprises the oligonucleotide overhang identification sequence (Column 2, Lines 57-58 and Column 11, Line 44—Column 12, Line 27).
Green does not explicitly teach one or more blocked nucleotides. Green does not teach or suggest an agent comprising a phosphatase activity.
Amorese teaches a plurality of oligonucleotides with a 5’ and/or 3’ overhang as well as oligonucleotides with no overhang (Column 8, Lines 21-45). Amorese teaches ligation products where non-complementary ends exist on each insert (Column 5, Lines 55-56, Column 18, Lines 3-13). Amorese teaches using an agent comprising a phosphatase activity (Column 8, Lines 58-60). Amorese teaches using one or more blocked nucleotides (Column 3, Lines 17-19, Column 13, Lines 14-16, Column 14, Lines 41-43 and Column 18, Lines 49-54) Amorese teaches using one or more blocked nucleotides allows for directional asymmetric ligation as well as to prevent polymerase extension which allows for selective target enrichment at a low cost and high throughput capture of genomic regions of interest without specialized instrumentation which can further allow for generation of a high efficiency nucleic acid library (Abstract, Column 2, Lines 23-29 Column 6, Lines 9-21, Column 3, Lines 17-19, Column 13, Lines 14-16 and Column 14, Lines 41-43).
As a common field of endeavor both Green and Amorese disclose kits and methods to generate a high efficiency nucleic acid library. It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Green with the teachings of Amorese to use one or more blocking nucleotides and an agent comprising phosphatase activity. This would allow for directional asymmetric ligation as well as to prevent polymerase extension which allows for selective target enrichment at a low cost and high throughput capture of genomic regions of interest without specialized instrumentation which can further allow for generation of a high efficiency nucleic acid library as taught by Amorese (Abstract, Column 2, Lines 23-29 Column 6, Lines 9-21, Column 3, Lines 17-19, Column 13, Lines 14-16 and Column 14, Lines 41-43).
Terminal Disclaimer
The terminal disclaimer filed on March 26, 2026 disclaiming the terminal portion of any
patent granted on this application which would extend beyond the expiration date of Patent 11,584,929 has been reviewed and is accepted. The terminal disclaimer has been recorded, and the nonstatutory double patenting rejections have been withdrawn.
Response to arguments
Applicant’s arguments and amendments filed March 12, 2026, with respect to the rejections under 35 U.S.C. § 112 (d) and 103 have been fully considered and are persuasive. Therefore, these rejections have been withdrawn.
However, upon further consideration, new rejections under 35 U.S.C. § 103 are set forth
above.
As discussed above, newly cited Green in view of newly cited Amorese, discloses an oligonucleotide overhang identification sequence specific to no overhang or one or more features of the oligonucleotide overhang as well as where the one or more features is the length of the overhang.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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