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 preciously canceled claims 1-7. Claims 8-23 are currently pending and under examination.
Information Disclosure Statement
The Information Disclosure Statements filed April 26, 2023; and April 04, 2024 have been considered.
Specification
The use of the terms Triton® X-100 and USER® (see Page 35, [00119], Page 38, [00130] and Page 51, [00185]-[00186]), which are trade names or a marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
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.
Claim 9 is 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 9 is considered vague and indefinite for the following reasons:
In claim 9, line 1, the terms “at least one enzyme… comprises uracil DNA glycosylase and an endonuclease” are unclear and confusing. The claim is unclear because it is not apparent how one enzyme could comprise both of said enzyme activities?
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 8-23 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. (WIPO International Application Publication WO 2007/010251 A2 published January 25, 2007), cited on the IDS filed April 26, 2023, in view of Gunderson et al. (WIPO International Application Publication WO 2016/075204 A1 published May 19, 2016), cited on the IDS filed April 26, 2023.
Regarding claim 8, Liu teaches a method of preparing nucleic acids for a sequencing reaction (Title and Abstract). Liu teaches providing an array comprising a plurality of amplification sites (Page 2, Second and Third Paragraph, Page 4, Last Paragraph—Page 5, First Paragraph and Page 43, First-Fourth Paragraph). Roy teaches the amplification sites comprise a plurality of capture nucleic acids attached to the amplification sites (Page 43, First-Fourth Paragraph). Liu teaches a first population of the plurality of capture nucleic acids comprises a cleavage site (Page 6, First-Third Paragraph). Liu teaches a plurality of clonal double-stranded modified target nucleic acids (Page 49, First Paragraph, Page 14, Last Paragraph—Page 15, Third Paragraph, Page 6, Third Paragraph and Page 14, First Paragraph). Liu teaches both strands of each double-stranded target nucleic acid are attached at their 5' ends to a capture nucleic acid (Page 6, First Paragraph, Page 12, Second—Third Paragraph and Page 45, First Paragraph) , Liu teaches one strand is attached to a capture nucleic acid that comprises the cleavage site (Page 7, Second Paragraph, Page 9, Second Paragraph, Page 14, Second Paragraph, Page 18, Second Paragraph and Page 47, First Two Paragraphs). Liu teaches the cleavage site is positioned in a double-stranded region of each double-stranded molecule (Figs. 1 and 2). Liu teaches contacting the array with a composition comprising at least one enzyme to produce an abasic site at the cleavage site (Page 7, Second Paragraph, Page 18, Last Paragraph and Claims 5 and 21). Liu teaches cleavage occurs at the cleavage site (Page 19, Second Paragraph). Liu teaches cleavage converts one strand of double-stranded target nucleic acids into a first strand attached to the amplification site and a second strand that is not attached to the amplification site (Abstract, Page 5, Second Paragraph and Figs. 1 and 3). Liu teaches single-stranded capture nucleic acids comprising a free 3' end (Page 9, Second Paragraph, Page 20, Second Paragraph, Page 21, Third Paragraph, Page 29, First Paragraph and Page 39, Second Paragraph).
Regarding claim 9, Liu teaches the at least one enzyme to produce an abasic site at the cleavage site comprises uracil DNA glycosylase and an endonuclease (Page 7, Second Paragraph).
Regarding claim 10, Liu teaches the endonuclease is DNA glycosylase- lyase Endonuclease VIII (Page 19, Second Paragraph).
Regarding claim 11, Liu teaches removal of the at least one enzyme to produce an abasic site at the cleavage site and the exonuclease from the array (Page 18, Last Paragraph—Page 19, Third Paragraph).
Regarding claim 12, Liu teaches subjecting the cleaved double-stranded target nucleic acids to conditions that remove the second strand that is not attached to the amplification site (Abstract, Page 5, Second Paragraph, Page 10, First Paragraph and Page 12, Second—Fifth Paragraph).
Regarding claim 13, Liu teaches the conditions that remove the second strand comprise a denaturant, and the denaturant results in immobilized single-stranded nucleic acids comprising a target nucleic acid covalently attached to a second population of capture nucleic acid, as well as the second population of capture nucleic acids is attached to the amplification sites (Abstract, Page 5, Second Paragraph and Page 12, Second—Fifth Paragraph, Page 45, Last Paragraph and Figs. 1A-1E).
Regarding claim 14, Liu teaches the denaturant comprises formamide (Page 76, Last Paragraph).
Regarding claim 15, Liu teaches re-annealing the immobilized single-stranded nucleic acid to a member of the first population of capture nucleic acids to generate an immobilized partially single-stranded nucleic acids (Page 30, Second and Last Paragraph).
Regarding claim 16, Liu teaches the cleavage site is positioned in the capture nucleic acid region of the double-stranded region of each double-stranded target nucleic acid (Figs. 1 and 2).
Regarding claim 17, Liu teaches the cleavage site comprises a uracil, wherein an abasic site is generated by the uracil DNA glycosylase, and wherein the abasic site is cleaved by the endonuclease (Page 7, Second Paragraph and Claims 5-6 and 21-22).
Regarding claim 18, Liu teaches the method of claim 8 as discussed above.
Regarding claim 19, Liu teaches hybridizing a sequencing primer to the immobilized single-stranded nucleic acids of claim 13 or a single stranded region of the immobilized partially single-stranded nucleic acids of claim 15, thereby preparing single-stranded nucleic acids for a sequencing reaction (Page 3, Second Paragraph, Page 8, Last Paragraph—Page 9, First Paragraph and Page 10, First Paragraph).
Regarding claim 20, Liu teaches performing a sequencing reaction to determine the sequence of at least one region of the immobilized single-stranded nucleic acids or the immobilized partially single-stranded nucleic acids (Page 30, Second Paragraph).
Regarding claim 21, Liu teaches the sequencing reaction comprises sequencing-by-synthesis (Page 46, Fourth Paragraph).
Regarding claim 22, Liu teaches the array is produced by amplifying a plurality of target nucleic acids using the capture nucleic acids as amplification primers (Page 8, Last Paragraph, Page 39, First Paragraph, Page 42, First Paragraph—Page 43, Second Paragraph).
Regarding claim 23, Liu teaches amplifying as discussed above.
Liu does not teach or suggest exonuclease comprising a 3' to 5' single-stranded DNA exonuclease activity Liu does not teach or suggest a single-stranded capture nucleic acids comprising a free 3' end are reduced in length by the exonuclease. Liu does not teach or suggest the exonuclease is exonuclease I. Liu does not teach or suggest amplifying comprises exclusion amplification.
Gunderson teaches arrays for producing and sequencing clusters of nucleic acids using bridge amplification and exclusion amplification (Title, Abstract, Pages 11-12, [0083]-[0085] and Pages 43-44, [00202]). Gunderson teaches providing an array with a plurality of amplification sites (Pages 43-44, [00202]-[00203]). Gunderson teaches capture nucleic acids attached to amplification sites (Page 1, [0003], Pages 7-9, [0065]-[0068], Page 13, [0093] and Fig. 1). Gunderson teaches capture nucleic acids comprise cleavage sites (Page 15, [00100], Pages 52-53, [00231] and Figs, 7B and 12A-B). Gunderson teaches a plurality of clonal double-stranded target nucleic acids (Page 11, [0083], Page 13, [0093] and Page 76, [00326]). Gunderson teaches both strands of each double-stranded target nucleic acid are attached at their 5' ends to a capture nucleic acid (Page 57, [0256], Page 59, [00262] and Figs. 2-4 and 7A-B). Gunderson teaches one strand is attached to a capture nucleic acid that comprises the cleavage site (Page 15, [00100] and Page 79, [00334]). Gunderson teaches the cleavage site is positioned in a double-stranded region of each double-stranded molecule (Page 15, [00100], Pages 52-53, [00231] and Figs, 7B and 12A-B). Gunderson teaches contacting the array with a composition comprising at least one enzyme to produce an abasic site at the cleavage site and an exonuclease comprising a 3' to 5' single-stranded DNA exonuclease activity (Pages 52-53, [00231], Page 15, [00109], Pages 18-19, [00118] and Page 77-78, [00330]). Gunderson teaches cleavage occurs at the cleavage site (Pages 52-53, [00231]). Gunderson teaches cleavage converts one strand of double-stranded target nucleic acids into a first strand attached to the amplification site and a second strand that is not attached to the amplification site (Fig. 7). Gunderson teaches single-stranded capture nucleic acids are reduced in length by the exonuclease (Pages 18-19, [00118], Page 54, [00236] and Pages 77-78, [00330]). Gunderson teaches that using the disclosed methods allows for advantageously carrying out rapid efficient multiplex formats such that multiple different target nucleic acids are manipulated simultaneously as well as providing for rapid and efficient detection (Page 104, [00399] and Pages 104-105, [00401]).
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 Liu with the teachings of Gunderson, using an exonuclease comprising a 3’ to 5’ single-stranded DNA exonuclease activity that reduces the length of the single-stranded nucleic acids. Using these methods would allow for advantageously carrying out rapid efficient multiplex formats such that multiple different target nucleic acids are manipulated simultaneously as well as providing for rapid and efficient detection as taught by Gunderson (Page 104, [00399] and Pages 104-105, [00401]).
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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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684