DETAILED ACTION
The amendment filed on 12/01/2025 has been entered.
Claim 1 is amended in the claim set filed on 12/01/2025.
Applicant’s election without traverse of Group I, (Claims 1-8 and 20-21) drawn to DNA Long Adapter Single Stranded Oligonucleotide (LASSO) probes and targets in the reply filed on 08/12/2025 is acknowledged. Applicant further elects ssDNA LASSO probe as the species. Claims 1-8 read on the election.
Claims 9-21 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group or species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 08/12/2025.
Claim 21 is canceled in the claim set filed on 12/01/2025.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Claims 1-8 in the claim set filed on 12/01/2025 are currently under examination.
Response to the Arguments
Objections to the Specification in the previously mailed non-final have been withdrawn in light of applicants incorporation of the abstract on a separate sheet.
Applicant’s arguments regarding previous rejection(s) of claim(s) 1-8 under 35 U.S.C. 103 have been fully considered and are not persuasive. Applicant’s argument on Pg. 12, states that The 35 U.S.C. 103 rejections documented in the previously mailed non-final have been maintained in light of applicants claim amendments and arguments on Pg. 8-11. As necessitated by amendment, revised rejection are made as documented below in the 35 U.S.C. 103 rejection in this office action on Pg. 3-6.
The rejections for claims 1-8 are documented below in this Final Office Action are necessitated by claim amendments filed on 12/01/2025.
Priority
This application claims priority to US Provisional Application No., 63/255,509 filed October 14, 2021. The priority date of claim set filed on August 12, 2025, is determined to be October 14, 2021.
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.
Claims 1-8 are rejected under 35 U.S.C. 103 as being unpatentable over Parekkadan et al. (“Parekkadan”; US Patent App. Pub. No. US 20180171386 A1, June 21, 2018).
Interpretation: Regarding claims 3 and 8, the limitation “or combinations thereof” renders the claim elements to read on at least one of the limitations claimed and optionally up to all recited limitations claimed.
Parekkadan discloses long adapter single strand oligonucleotide (LASSO) probes that can be used to capture and clone thousands of kilobase-sized DNA fragments in a single reaction, as well as method of generating the same. (Abstract)
Regarding claim 1, Parekkadan teaches a LASSO probe comprising “Long Adapter Single Stranded Oligonucleotides (LASSOS) comprising, from 5′ to 3′: a ligation arm sequence … complementary to a 5′ region of a target sequence (i.e., a single contiguous target sequence, e.g., a genomic sequence, lncRNA, cDNA or other); a Long Adapter sequence … comprising a fusion overlapping sequence and optionally one or more restriction enzyme recognition sites; an extension arm sequence … complementary to a 3′ region of a target sequence, wherein the ligation arm and extension arm sequences are complementary to 5′ and 3′ regions of a single target sequence and the complementary regions are at least 200-30,000 nts apart... and wherein the Long Adapter sequence is not complementary to the target sequence.” (Para.6). “fusion overlapping sequence” reads on DNA recombinase recombination site. Thus, Parekkadan teaches a single stranded (ss) DNA Long Adapter Single Stranded Oligonucleotide (LASSO) probe, comprising, from 5' to 3':a ligation arm sequence complementary to a 5' region of a target sequence; a backbone sequence that is not complementary to the target sequence, and comprises a recombination site; and an extension arm sequence complementary to a 3' region of the target sequence, wherein the ligation arm sequence and extension arm sequence are complementary to 5' and 3' regions of a single target sequence, respectively, and the complementary regions are at least 200 nucleotides (nts) apart on the target sequence.
Regarding claim 2, Parekkadan teaches a LASSO probe wherein “the target sequence is a coding or noncoding DNA sequence” (Para. 7). Thus, Parekkadan teaches a LASSO probe wherein the target sequence is a coding or noncoding DNA sequence.
Regarding claim 3, Parekkadan teaches a LASSO probe wherein “a ligation arm sequence of 20-40, 15-80, nucleotides (nt)” (Para. 6). Parekkadan teaches a LASSO probe wherein “a Long Adapter sequence of 200 to 2500 nt, e.g., … 200-800 nt” (Para. 6). Parekkadan teaches a LASSO probe wherein “an extension arm sequence that is 15-80 nt, preferably 20-40 nt long” (Para. 6). “15-80” comprises the claimed 20 to 50 nts. Thus, Parekkadan teaches a LASSO probe wherein the ligation arm sequence is about 20 to 50 nts; the backbone sequence is about 200 to 800 nts; the extension arm sequence is about 20 to 40 nts; or combinations thereof.
Regarding claim 4, Parekkadan teaches a LASSO probe wherein “the Long Adapter Oligonucleotides comprise a sequence of 200 to 2500 nt, e.g., 200-500, 200-2000, 200-2500, 200-1500, 200-1000, or 200-800 nt” (Para. 12). “200 to 2500, 200-2000, 200-2500, 200-1500, 200-1000, or 200-800 nt” comprise the claimed about 400 to 800 nts. Thus, Parekkadan teaches a LASSO probe wherein the ssDNA LASSO is about 400 to 800 nts.
Regarding claim 5, Parekkadan teaches a LASSO probe wherein “a single contiguous target sequence” (Para. 6). Thus, Parekkadan teaches a LASSO probe wherein the target sequence is a single contiguous target sequence.
Regarding claim 6, Parekkadan teaches a composition comprising wherein “LASSO oligonucleotides, wherein... oligonucleotides with sequences complementary to 10 or more … different target sequences” (Para. 8). Thus, Parekkadan teaches a composition comprising a LASSO probe wherein the plurality includes oligonucleotides with sequences complementary to at least two different target sequences.
Regarding claim 7, Parekkadan teaches a composition comprising “one or more of the LASSO… probes described herein, and optionally one or more additional reagents ” (Para. 26). Thus, Parekkadan teaches a composition comprising one or more ssDNA LASSO probes of one or more ssDNA LASSO probes of a pharmaceutically acceptable carrier.
Regarding claim 8, Parekkadan teaches a kit comprising one or more of the LASSO… probes described herein, and optionally one or more additional reagents” (Para. 26). Parekkadan also teaches a kit comprising “LASSO Probes” (Para. 58), “DNA Polymerase” (Para. 62), “Thermo stable DNA Ligase” (Para. 63), “dNTPs” (Para. 64), “Exonuclease I …Exonuclease III … Lambda Exonuclease” (Para. 66-68), and Post Capture PCR master mix with primers … DNA polymerase … dNTPs …Primers for Post Capture PCR” (Para. 69-72). Thus, Parekkadan teaches a kit comprising one or more ssDNA LASSO probes of one or more ssDNA LASSO probes of one or more endonucleases, one or more exonucleases, one or more polymerases, one or more ligases, one or more recombinases; one or more reagents for PCR, or combinations thereof.
Therefore, the invention as recited in claims 1-8 are prima facie obvious over the prior art Parekkadan et al. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to have a single stranded (ss) DNA Long Adapter Single Stranded Oligonucleotide (LASSO) probe according to the limitations of the instant application claims 1-5; a composition according to the limitations of the instant application claims 6-7; and a kit according to the limitations of the instant application claim 8 based on Parekkadan et al. (US Patent App. Pub. No. US 20180171386 A1).
Response to Arguments
Applicant' s arguments filed 12/01/2025 (Pg.8-11) with respect to claims 1-8 have been considered but are not persuasive. To clarify some instances argued in the response filed 12/01/2025 see responses to each argument made by Applicant below:
Applicants’ argument: “Parekkadan cannot render the amended claims prima facie obvious at least because Parekkadan does not teach each element of amended claim 1. The "fusion overlapping sequence" of Parekkadan is clearly different from the "DNA recombinase recombination site" recited in amended claim 1…nothing in Parekkadan would give a person of ordinary skill in the art any reason or motivation to add a DNA recombinase recombination site to its LASSO probe, because Parekkadan never uses or even mentions DNA recombinases. Therefore, the present claims are not prima facie obvious over Parekkadan. Withdrawal of the obviousness rejection is requested.” (Pg. 9)
Response: In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., The "DNA recombinase recombination site" is a site that acts as a target for a site-specific DNA recombinase, such as a Cre recombinase or Flp recombinase, that mediates DNA recombination at the site. See e.g., FIGs. 1A, 2A, and 10B; and paragraphs [0017], [0031], [0114], [0123], and [0314] of the application as filed.) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Furthermore, the claims do not explicitly define DNA recombinase recombination site, thus the claim encompasses a broader aspect which is made obvious over the "fusion overlapping sequence” taught by Parekkadan.
Applicants’ argument: “II. The claimed LASSO probes achieve unexpected and superior effects. Any prima facie case of obviousness, should it exist (which Applicant does not concede), is rebutted by the unexpected and superior effects demonstrated for the claimed LASSO probes. The inclusion of a DNA recombinase recombination site in the LASSO probes allow the probes to be manufactured more efficiently and with higher quality. The claimed LASSO probes achieve unexpected and superior effects in facilitating manufacturing processes, enabling production of the probes at significantly higher efficiency, and with significantly higher purity and capture efficiency.” (Pg. 9-10)
Response: In response to applicant's argument that ” LASSO probes achieve unexpected and superior effects”, a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim. Furthermore, the invention is a structure and can be used for anything, thus the unexpected results argument is not persuasive.
Applicants’ argument: “Applicant submits that the product claims (claims 1-8) are in condition for allowance. Therefore, Applicant requests rejoinder and examination of the withdrawn method claims (claims 9-20).” (Pg. 11)
Response: In response to applicant's request for rejoinder, no claims are in condition for allowance, therefore the claims cannot be rejoined in this Final office action.
Conclusion of Response to Arguments
In view of the amendments, revised rejections and above responses to arguments are documented in this Final Office Action. No claims are in condition for allowance.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Tosi, L., Sridhara, V., Yang, Y., Guan, D., Shpilker, P., Segata, N., Larman, H. B., & Parekkadan, B. (2017). Long-adapter single-strand oligonucleotide probes for the massively multiplexed cloning of kilobase genome regions. Nature biomedical engineering, 1, 0092. (Pg. 5, Para. 3 – Claim 1, recombination site)
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682