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 .
DETAILED ACTION
Pursuant to a preliminary amendment filed September 21, 226, claims 47 and 52-70 are currently pending in the instant application.
Response to Election/Restriction
Applicant's election of Group IV, without traverse, claims 47-51 directed to a method for correcting nucleotide sequence errors in assembled nucleic acid molecules; and Applicant’s election of Species without traverse, as follows:
Species (D): further comprising in step (d) contacting the reannealed assembled nucleic acid molecules with: (ii) at least one mismatch repair binding protein, etc. (claim 50), in the reply filed July 13, 2026, is acknowledged.
Supplemental Election of Species
Applicant’s election of Species for new claims 52-70 in the Office Action mailed July 29, 2026 without traverse, as follows:
Species (A): wherein the second error-correction step comprises: (d)(i) denaturing and reannealing the first error-corrected assembled nucleic acid molecules…into second error-corrected assembled nucleic acid molecules (claim 47),
Species (B): wherein the synthetically produced nucleic acid molecules are chemically synthesized nucleic acid molecules (claim 52), and
Species (C): wherein the second error correction step is the mismatch repair endonuclease of step (d)(i) (claim 60), in the reply filed September 21, 2026 is acknowledged.
Claims 46(d)(ii), 53-56 and 63-70 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.
Please Note: in the reply filed July 13, 2026, for Species (D) Applicant elected claim 50 (e.g., further comprising in step (d) contacting the reannealed assembled nucleic acid molecules with…nucleic acid molecules not containing mismatches (claim 50). Claims 56, 67 and 70 recite the method of claim 47 further comprising an additional step (e.g., before the pooling step, the nucleic acid molecules are amplified (claim 56); further comprising amplifying the second error-corrected assembled nucleic acid molecules (claim 67); and further comprising introducing the error-corrected assembled nucleic acid molecules into a target vector (claim 70).
Claims 56, 67 and 70 are withdrawn as being directed to a non-elected species. Claims 68 and 69 are withdrawn as depending from a withdrawn claim.
The restriction requirement is still deemed proper and is therefore made FINAL.
The claims will be examined insofar as they read on the elected species.
Therefore, claims 47, 52 and 57-62 are under consideration to which the following grounds of rejection are applicable.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on November 29, 2023 and April 9, 2026 have been considered. Initialed copies of the IDSs accompany this Office Action.
Priority
The present application filed August 17, 2023 is a CON of US Patent Application 16518099, filed July 22, 2019, which is a DIV of US Patent Application 14964060, filed December 9, 2015 (now US10407676), which claims the benefit of US Provisional Patent Application 62145359, filed April 9, 2015; and US Provisional Patent Application 62089590, filed December 9, 2014.
Claim Objections/Rejections
Claim Objections
Claims 58, 59, 61 and 62 are objected to because of the following informalities: Claims 58, 59, 61 and 62 recite terms such as “RES I”, and “PBCV-1 DNA ligase”, where an abbreviation should be spelled out in the first encounter of the claims.
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 47, 52 and 57-62 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 47 is indefinite for the recitation of the term “the assembled nucleic acid molecules” such as recited in claim 47, lines 8-9. There is insufficient antecedent basis for the term “the assembled nucleic acid molecules” in the claim.
Claim 47 is indefinite for the recitation of the term “thereby forming a first error-correction product comprising cleaved nucleic acid molecules” such as recited in claim 47, lines 16-17 because claim 47 does not recite “cleaving” reannealed assembled nucleic acid molecules comprising mismatches. Instead, claim 47, line 15 recites “under conditions suitable for cleavage”, such that claim 47 does not actually recite “cleaving” and, thus, the metes and bounds of the claim cannot be determined.
Claim 47 is indefinite for the recitation of the term “reassemble cleaved nucleic acid molecules generated by the cleavage” such as recited in claim 47, lines 18-19 because claim 47 does not recite a step of cleaving and, thus, the metes and bounds of the claim cannot be determined.
Claim 47 is indefinite for the recitation of the term “further cleaved nucleic acid molecules” such as recited in claim 47, lines 28 and 29 because claim 47 does not actually recite that the second reannealed assembled nucleic acid molecules are cleaved. Claim 47 merely recites that they are contacted with at least one mismatch repair endonuclease and, thus, the metes and bounds of the claim cannot be determined.
Claim 47 is indefinite for the recitation of the term “the error rate” such as recited in claim 47, line 40. There is insufficient antecedent basis for the term “the error rate” in the claim.
Claims 57-62 are indefinite for the recitation of the term “step” (x) such as recited in claim 57, line 1. There is insufficient antecedent basis for the term “step” (x) in the claim because claim 47, lines 7, 10 and 21 recite the terms (a), (b), (c), (d); “first error correction step” and “second error correction step”.
Claim 52 is indefinite insofar as it ultimately depends from instant claim 47.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 57-62 are rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 57-62 recite (in part): “step (x)” such as recited in claim 57, line 1 because claim 57 depends from instant claim 47, wherein claim 47, lines 7, 10 and 21 recite the terms (a), (b), (c), (d); “first error correction step” and “second error correction step”. Thus, claims 57-62 are improper dependent claims for failing to further limit the subject matter of the claim upon which they depend, or for failing to include all the limitations of the claim upon which they depend.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 102
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 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 47, 52 and 57-62 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Peterson et al. (hereinafter “Peterson”) (US Patent Application Publication No. 20130109596, published May 2, 2013; effective filing date September 26, 2011).
Regarding claim 47, Peterson teaches compositions and method for the synthesis of nucleic acid molecules (interpreted as synthetically produced nucleic acid molecules, claim 47) (paragraph [0004]). Peterson teaches a method comprising one or more of the following steps: (a) synthesizing a plurality of nucleic acid molecules, wherein each nucleic acid molecule is prepared in a microquantity in the well of a plate; (b) combining the nucleic acid molecules generated in (a), or a portion thereof, to produce a pool (interpreted as pooling); (c) joining some or all of the nucleic acid molecules present in the pool formed in (b) to form a plurality of larger nucleic acid molecules (interpreted as joining); (d) eliminating nucleic acid molecules which contain sequence errors from the plurality of larger nucleic acid molecules formed in (c) to produce an error corrected nucleic acid molecule pool (interpreted as conducting error correction); and (e) assembling the nucleic acid molecules in the error corrected nucleic acid molecule pool to form the assembled nucleic acid molecule (interpreted as pooling), wherein the joining of nucleic acid molecules present in the pool will be mediated by polymerase chain reaction (PCR) (interpreted as amplifying by PCR); and step (b) can further comprise combining nucleic acid molecules generated in (a) with nucleic acid molecules obtained by other means to form a pool, wherein said other means include PCR, restriction enzyme digest or exonuclease treatment (interpreted as denaturing and reannealing; contact with a mismatch repair endonuclease; amplifying, and producing a first error-corrected nucleic acid molecules, claim 47) (paragraphs [0013]-[0019]). Peterson teaches that the nucleic acid molecules then move on to another digital PCR station 1610 and again cycle between cooling and heating blocks, wherein an error correction reaction can occur in digital PCR station 1610 (interpreted as conducting (d)(i) including denaturing and reannealing using the first error-corrected nucleic acid molecules to produce second error-corrected nucleic acid molecules, claim 47) (paragraph [0286]). Peterson teaches in Figure 16, a diagram of the processing nucleic acid molecules, wherein carrier oil is transported past a series of additional reservoirs 1602 that contain reagents, wherein the circular structures represent individual reagents reservoirs, such that exemplary reagents include nucleic acid molecules, PCR enzymes, primers, and vectors; as well as, other Module 3 related components, wherein reagents transported by the carrier oil are then transported to a mixing chamber 1603 where mixing occurs; such that the reagents then move on to a digital PCR station 1604; and the tube 1601 travels between a heating block 1605 where denaturation occurs followed by a cooling block 1606 where annealing and PCR occurs, wherein each time a vesicle travels to the cooling block 1606 after the first time, a PCR amplification occurs and, after exiting the digital PCR station 1604, the vesicles move past additional reagent reservoirs 1607 for the optional addition of more reagents, (e.g., buffers, error correction components, etc), then on to another optional mixing chamber 1608, where the vesicle then move on to an optional storage location 1609 ; and the nucleic acid molecules then move on to another digital PCR station 1610 and again cycle between cooling and heating blocks, wherein an error correction reaction can occur in digital PCR station 1610 (interpreted as steps (a)-(c) including pooling, assembling, conducting error-protection step by denaturing, contact with an enzyme, and amplifying, then conducting (d)(i) using the first error-corrected nucleic acid molecules to produce second error-corrected nucleic acid molecules, claim 47) (paragraphs [0283]-[0286]; and Figure 16). Figure 16 is shown below:
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Peterson teaches that the error correction processes include the use of one or more mis-match repair endonucleases (interpreted as at least one error correction endonucleases, claim 47) (paragraph [0028], lines 4-7). Peterson teaches that the product nucleic acid molecule contains less than one sequence error per kilobase (interpreted as encompassing an error rate is between one base in 2,000 to one base in 30,000, claim 47) (paragraph [0027], lines 4-5). Peterson teaches that all nucleic acid molecules required for assembly of a full-length construct can be synthesized on a single array (interpreted as pooling synthetically produced nucleic acid molecules, claim 47) (paragraph [0184]). Peterson teaches that in a process described in the Yang et al. paper, a linear vector is mixed with double stranded nucleic acid molecules which share sequence homology at the termini, wherein an enzyme with exonuclease activity (i.e., T4 DNA polymerase, T5 exonuclease, T7 exonuclease, etc.) is added which peels back one strand of all termini present in the mixture (interpreted as terminal regions of homology, claim 47) (paragraph [0216], lines 1-6). Peterson teaches in Figure 11, where the blocks on each end of the nucleic acid molecule represent nucleic acid segments which facilitate joining (e.g., Gateway sites, regions of homology, etc.) (interpreted as terminal regions of homology, claim 47) (paragraph [0076]; and Figure 11). Figure 11 is shown below:
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Peterson teaches that nucleic acid molecules introduced into cells for assembly will normally have certain features which allow them to be assembled in a particular order, wherein one feature is terminal sequence homology between nucleic acid molecules being assembled (interpreted as at least one molecule shares at least one terminal region of sequence homology with a terminal region of another nucleic acid molecule, claim 47) (paragraph [0255]).
Regarding claim 52, Peterson teaches that a number of methods of general chemistries and chemical methods are known in the art for synthesizing nucleic acid molecules (interpreted as chemically synthesized nucleic acid molecules, claim 52) (paragraph [0346], lines 1-3).
Regarding claim 57, Peterson teaches that nicks in the resulting nucleic acid molecules can be repaired by introduction of the molecule into a cell or by the addition of ligase (interpreted as ligase-mediated ligation of 5’-phosphoylated, claim 57) (paragraph [0216], lines 10-12). Peterson teaches the assembly of chemically synthesized nucleic acid molecules based on the direct ligation of overlapping pairs of 5'-phosphorylated nucleic acid molecules ("ligation-based assembly"), wherein single-stranded nucleic acid molecules are synthesized, phosphorylated and annealed to form double-stranded molecules with complementary overhangs (e.g., overhangs of four nucleotides (interpreted as ligase-mediated ligation of 5’-phosphoylated, claim 57) (paragraph [0223], lines 1-8).
Regarding claims 58, 60 and 61, Peterson teaches that the second set of full-length molecules are reacted with one or more endonucleases to yield a third set of molecules intended to have lengths less than the length of the complete desired gene sequence, such that the endonucleases cut one or more of the molecules in the second set into shorter molecules the molecules are cut with T7 endonuclease I (interpreted as T7 endonuclease I; and error correction step (d)(i), claims 58 and 60) (paragraph [0233], lines 1-6 and 11-12).
Regarding claims 59 and 62, Peterson teaches that one error correction method comprises: denaturing DNA contained in a reaction buffer, and T7 endonuclease I and DNA ligase are added to the solution (interpreted as DNA ligase, claim 59) (paragraph [0240]).
Peterson does not specifically exemplify T4 DNA ligase, etc. (claim 59).
Peterson meets all the limitations of the claims and, therefore, anticipates the claimed invention.
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 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.
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 47, 52 and 57-62 are rejected under 35 U.S.C. 103 as being unpatentable over Peterson et al. (hereinafter “Peterson”) (US Patent Application Publication No. 20130109596, published May 2, 2013; effective filing date September 26, 2011) in view of Pushkarev et al. (hereinafter “Pushkarev”) (US Patent No. 9725765, issued August 8, 2017; and US20130257870, published June 20, 2013).
The teachings of Peterson as applied to claims 47, 52 and 57-62 are described supra.
Peterson does not specifically exemplify T4 DNA ligase, etc. (claims 59 and 62, both in part).
Regarding claims 59 (in part) and 62 (in part), Pushkarev teaches methods for the detection of genetic variants (col 44, lines 7-8). Pushkarev teaches that nucleic acid obtained from biological samples typically is fragmented to produce suitable fragments for analysis; where template nucleic acids can be fragmented or sheared to desired length, using a variety of mechanical, chemical and/or enzymatic methods (col 15, lines 33-37). Pushkarev teaches that the fragments are amplified after partitioning, wherein any amplification method known in the art can be used in amplification techniques including, but not limited to, quantitative PCR, quantitative fluorescent PCR (QF-PCR), multiplex fluorescent PCR (MF-PCR), real time PCR (RTPCR), single cell PCR, restriction fragment length polymorphism PCR (PCRRFLP), PCK-RFLPIRT-PCR-IRFLP, hot start PCR, nested PCR, in situ polonony PCR, in situ rolling circle amplification (RCA), bridge PCR, picotiter PCR and emulsion PCR, ligase chain reaction (LCR), transcription amplification, self-sustained sequence replication, selective amplification of target polynucleotide sequences, consensus sequence primed polymerase chain reaction (CP-PCR), arbitrarily primed polymerase chain reaction (AP-PCR), DOP-PCR and NABSA (interpreted as amplification by PCR to reassembled nucleic acid molecules ) (col 16, lines 33-48). Pushkarev teaches methods for joining two polynucleotides are known in the art, and include without limitation, enzymatic and nonenzymatic (e.g. chemical) methods (col 19, lines 23-24). Pushkarev teaches multiple ligases, each having characterized reaction conditions, are known in the art, and include, without limitation NAD+-dependent ligases including tRNA ligase, Taq DNA ligase, Thermus filiformis DNA ligase, Escherichia coli DNA ligase, Tth DNA ligase, Thermus scotoductus DNA ligase (I and II), thermostable ligase, Ampligase thermostable DNA ligase, VanC-type ligase, 9°N DNA ligase, Tsp DNA ligase, and novel ligases discovered by bioprospecting; ATP-dependent ligases including T4 RNA ligase, T4 DNA ligase, T3 DNA ligase, T7 DNA ligase, Pfu DNA ligase, DNA ligase 1, DNA ligase III, DNA ligase IV, and novel ligases discovered by bioprospecting; and wild-type, mutant isoforms, and genetically engineered variants thereof, wherein ligation can be between polynucleotides having hybridizable sequences, such as complementary overhangs (interpreted as T4 DNA ligase and Taq ligase, claim 59 and 6) (col 19, lines 35-50). Pushkarev teaches that overlapping fragments can be computationally discarded since they no longer represent the same initial long molecule, such that this process allows to treat a population of molecules resulting after amplification as a clonally amplified population of disjoint molecules with no significant overlap or homology, which enables sequencing errors to be corrected to achieve very high consensus accuracy and allows unambiguous reconstruction of long fragments, wherein if overlaps are not discarded, then one can take into consideration that reads can be originating from fragments originating from two homologous chromosomes or overlapping regions of the same chromosome (in case of diploid organism) which makes error correction difficult and ambiguous (col 39, lines 15-22). Pushkarev teaches that detection of large-scale structural variants and/or losses of heterozygosity is often crucial for cancer genome sequencing, as well as the ability to differentiate between somatic variants and errors in base calling (col 45, lines 45-50).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of annealing nucleic acid molecules using a ligase as exemplified by Pushkarev, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of highly efficient, small volume nucleic acid synthesis comprising error-correction methods including the steps of pooling, denaturing, and assembling the nucleic acid molecules, followed by treatment with a mis-match repair endonuclease and a DNA ligase as disclosed by Peterson, to include the selection and/or replacement of the DNA ligase of Peterson with T4 DNA ligase and/or Taq polymerase in the method of improving re-sequencing accuracy and/or sequence alignment as taught by Pushkarev with a reasonable expectation of success in eliminating nucleic acid sequence errors by providing product nucleic acid molecules that contain less than one sequence error per kilobase; in improving the detection of sequence variants; and/or in selecting a mis-match repair ligase for use in joining polynucleotides under suitable reaction conditions for the correction of nucleotide sequence errors.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly
rejected under 35 USC §103 as obvious over the art.
Conclusion
Claims 47, 52 and 57-62 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally be reached on Monday-Friday (6am-2:30pm).
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/AMY M BUNKER/
Primary Examiner, Art Unit 1684
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