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 the species: (i) the single specific base dU in claim 6 and (ii) the restriction endonuclease recognition site in claim 12 in the reply filed on 05/28/2026 is acknowledged.
Claims 7, 9-11, and 14 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 1-18, 20-21 are pending.
Claims 1-6, 8, 12-13,15-18, and 20-21 are under examination on the merits.
Priority
This application 18/570,440 filed on 12/14/2023 is a 371 national phase of PCT/CN2021/100436 filed on 06/16/2021.
The priority date of claim 1 and its dependent claims is determined to be 06/16/2021, the filing date of PCT/CN2021/100436.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The use of terms which are trade names or marks used in commerce (including Qubit™, NEB®, among others), has been noted in this application. The term 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 Objections
Claims 1, 15, and 16 objected to because of the following informalities: Claim 1 recites “single-stranded rolling circle amplification” in the preamble. Claims 1, 15, and 16 recites the limitation “the rolling circle amplification”. For purposes of examination it is interpreted that the rolling circle amplification of claims 1, 15, and 16, are the single-stranded rolling circle amplification recited in the preamble of claim 1. It is suggested to make the recited terms consistent. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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 1-6, 8, 12-13,15-18, and 20-21 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 the steps “i) subjecting a single-stranded circular DNA to the rolling circle amplification with a first primer to obtain an amplified sequence, wherein the first primer is complementary to a partial region of the single-stranded circular DNA, and the single-stranded circular DNA possesses a disconnection mechanism to open the single-stranded circular DNA; ii) opening the single-stranded circular DNA through the disconnection mechanism, to obtain a single-stranded linear DNA; and iii) performing amplification with the single-stranded linear DNA as a second primer and the amplified sequence obtained in step i) as a template to obtain an amplified double-stranded sequence”. It is unclear if step ii) is required to occur after step i), or in parallel to step i).
Claim 1 recites the limitations “subjecting a single-stranded circular DNA to the rolling circle amplification with a first primer to obtain an amplified sequence” and “the amplified sequence obtained in step i) as a template”. It is unclear if the amplified sequence obtained in i) is required to be a single-stranded sequence. Addition of the words single-stranded would clarify the limitation.
Claims 2-6, 8, 12-13,15-18, and 20-21 are similarly indefinite because they directly or indirectly depend from claim 1.
Claim 5 recites the limitation "the specific base". There is insufficient antecedent basis for this limitation in the claim. No prior claim which claim 5 depends from recites a specific base.
Claims 6 and 8 are similarly indefinite because they directly or indirectly depend from claim 5.
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.
Claims 1-5 and 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (US20050069938) in view of Beals et al. (A mechanism for ramified rolling circle amplification. BMC Mol Biol. 2010. 11:1-10).
Regarding claim 1, Wang teaches methods for rolling circle amplification. Wang teaches a method comprising circularizing target nucleic acid molecules using linkers that comprise defined sequences, including restriction endonuclease sites (a disconnection mechanism) (para 14). The method may be used to circularize single strand DNA (para 19). Wang teaches amplifying the circularized nucleic acid molecule by rolling circle amplification (para 13) using primers (a first primer) (para 17) complementary to a region of the circularized nucleic acid (see examples Fig. 5).
Wang teaches the defined sequences (disconnection mechanism), such as restriction endonuclease sites, may be used later in amplification (para 14). Wang teaches the circular nucleic acid molecules can be cut to from linear products, which can be amplified with PCR (para 64). Use of restriction endonuclease sites reads on linearizing (opening) the circularized nucleic acid to obtain a single-stranded linear DNA. Wang further teaches primers can be used to generate double stranded copies (para 17), i.e. performing amplification to obtain an amplified double-stranded sequence .
Wang teaches the addition of restriction endonuclease sites, and cutting the circular nucleic acid to form a linear product (para 64) but does not teach using the single-stranded linear DNA obtained from opening the circularized nucleic acid as a primer in amplification as a second primer and the amplified sequence obtained in step i) to obtain an amplified double-stranded sequence.
Beals teaches a method for ramified rolling circle amplification. The method comprises using two primers to create a series of double-stranded DNA products to provides exponential DNA amplification under isothermal conditions (Abstract). Beals teaches a forward primer (first primer) that anneals to a ssDNA circular template to perform rolling circle amplification and produce a primary transcript (amplified sequence) (p. 2, col. 2 and Fig. 2). Beals further teaches using a second reverse primer comprising sequences corresponding to the ssDNA circular template to generate amplified double-stranded sequences using the primary transcript (amplified sequence) as template (Fig. 2).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Wang and Beals to arrive at the instantly claimed invention. The modification would have entailed using a second primer corresponding to the circular template as taught by Beals in the method of Wang. One would have been motivated by the advantages of two-primer ramified rolling circle amplification, namely exponential DNA amplification under isothermal conditions. One of skill in the art would have recognized that the linear product generated by cutting the circular template of Wang could be used as the second primer of Beals. This modification would have the added advantage of not requiring the addition of a second primer to the reaction, thus simplifying the reaction. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 2, Wang teaches circularizing target nucleic acid molecules DNA or cDNA) using linkers (adapter connection) (para 14, Fig. 5).
Regarding claim 3, Wang teaches primers for RCA (the first primer) can be RNA or DNA (Fig. 5, paras 116-120).
Regarding claim 4, Wang teaches the defined sequence of a restriction endonuclease site added during circularization (para 14) and further teaches cutting the circular nucleic acid to form a linear product (para 64), which reads on the disconnection mechanism is to open the single-stranded circular DNA through a specific region in the single-stranded circular DNA, wherein the specific region is broken in response to a biochemical reaction.
Regarding claim 5, Wang teaches addition of a defined sequence such as a restriction endonuclease site (para 14), which reads on a specific region comprising a specific sequence.
Regarding claim 12, Wang teaches addition of a defined sequence such as a restriction endonuclease site (para 14).
Regarding claim 13, Wang is silent regarding the identity of the restriction endonuclease recognition site.
However, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Wang and Beals to arrive at the instantly claimed invention. Determining an appropriate restriction endonuclease recognition site is deemed merely a matter of judicious selection and routine optimization which is well within the purview of the skilled artisan. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Claims 6 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (US20050069938) in view of Beals et al. (A mechanism for ramified rolling circle amplification. BMC Mol Biol. 2010. 11:1-10) as applied to claims 1-5 and 12-13 above, and further in view of Jiang et al. (US20170355981).
Regarding claims 6 and 8, Neither Wang nor Beals teach the specific base is a dU (claim 6) which is recognized and cleaved by uracil-DNA glycosylase (UDG) or apyrimidinic endonuclease 1 (APE1), to open the single-stranded circular DNA (claim 8).
It is noted that the specific base of claims 6 and 8 is not required by claim 5, which claims 6 and 8 depend from. Claim 5 requires “the specific region comprises one or both of the specific base and specific sequence.”
Jiang teaches a method for constructing a nucleic acid double-linker single-strand cyclic library, the method comprising a U nucleobase (dU) on a primer and using USER enzyme (which comprises Uracil DNA glycosylase) to cleave the sequence (Abstract).
Jiang teaches the U base is in the primer and does not teach the dU is the specific region in the single-stranded circular DNA.
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Wang and Beals with Jiang to arrive at the instantly claimed invention. The modification would have entailed selecting the dU base as the defined sequence in the linker used for circularizing the nucleic acid molecule in Wang. Wang teaches the use of restriction endonuclease sites. The mechanisms of dU and USER digestion are functionally the same as the use of restriction enzymes on restriction enzyme recognition sites. Using dU and UDG as substitutes for a restriction endonuclease site and restriction enzyme respectively would have been a matter of judicious selection and routine optimization which is well within the purview of the skilled artisan. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Claim 15-18 and 20-21 are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (US20050069938) in view of Beals et al. (A mechanism for ramified rolling circle amplification. BMC Mol Biol. 2010. 11:1-10) as applied to claims 1-5 and 12-13 above, and further in view of Joun et al. (US20150361481).
Regarding claim 15, neither Wang nor Beals teach adding the recited reagents during or after subjecting the single-stranded circular DNA to the rolling circle amplification.
Joun teaches reactions for nucleic acid amplification (abstract), including for sequencing library preparation (paras 489, 575). Joun teaches the amplified populations of target nucleic acids can be formed by conducting rolling circle amplification (para 221). Joun further teaches adding accessory proteins, buffers and compositions to amplification reactions including single-stranded binding protein and Tris buffers (para 521) and pyrophosphatase (para 554).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Wang and Beals with Joun to arrive at the instantly claimed invention. Joun teaches the addition of compositions, primers, enzymes, reagents, cofactors, buffers, and proteins as appropriate to different amplification reactions. Determining the appropriate combination would have been a matter of routine optimization well within the purview of one skilled in the art. As taught by Wang and Beals, rolling circle amplification was well known and conventional to those of skill in the art before the filing date of the claimed invention.. One of skill in the art would have known to select the appropriate reaction mixture as suggested by Jon. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claims 16 and 17, neither Wang nor Beals teach adding a helicase.
Joun teaches amplification reactions can include a helicase (para 39), which reads on adding a helicase during rolling circle amplification.
Joun is silent as to the type of helicase.
However, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Wang and Beals with Joun to arrive at the instantly claimed invention. The modification would have entailed adding a helicase as required for the amplification method. Joun teaches a wide-range of components for amplification reactions. Selecting the appropriate accessory proteins such as a type A helicase for the preferred amplification reaction would have been a matter of routine optimization and judicious selection. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claims 18, and 20-21, Wang teaches the method is an improved procedure for cDNA library construction (para 3) .
Regarding claim 18, Wang and Beals teach obtaining an amplified double-stranded sequence as recited in the rejection for claim 1.
Wang does not explicitly teach subjecting the amplified double-stranded sequence to sequencing library construction, to obtain the nucleic-acid sequencing library.
Joun teaches reactions for nucleic acid amplification (abstract), including for sequencing library preparation (paras 489, 575).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Wang and Beals with Joun to arrive at the instantly claimed invention. The modification would have entailed using the double-stranded amplified products of Wang and Beals with the method of Joun to prepare a library for sequencing. One of skill in the art would have been motivated to perform library preparation in order to make a sequencing library for detecting the amplified target nucleic acid molecules (a goal of Wang stated in the abstract). There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 20, Wang teaches obtaining full-length cDNA with the method as an improved procedure for cDNA library construction (para 3), which reads on a nucleic-acid sequencing library that is an mRNA full-length transcript library.
Regarding claim 21, Wang and Beals in view of Joun teach obtaining a nucleic-acid sequencing library according to claim 18 as described above.
Joun teaches library preparation (para 575) and further teaches sequencing the library (para 590).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Wang and Beals with Joun to arrive at the instantly claimed invention. The modification would have entailed adding the step of sequencing the sequencing library as taught by Joun to the method of Wang and Beals. . One of skill in the art would have been motivated to sequence the library in order to detect the amplified target nucleic acid molecules (a goal of Wang stated in the abstract). There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA GRAY whose telephone number is (571)272-0116. The examiner can normally be reached Monday-Friday 8-5 with second Fridays off.
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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
Prosecution Insights