The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s election of Group I, claims 23-28, in the reply filed on January 15, 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 1-22 are canceled. Claims 29-41 have been withdrawn from further consideration by the examiner because they are drawn to non-elected inventions. Claims 23-28 are under consideration.
Priority: This application is a 371 of PCT/SG2021/050593, filed October 1, 2021, which claims benefit to foreign application SG 10202009842T, filed October 2, 2020. A copy of the foreign priority document has been received in the instant application on March 31, 2023, and is in the English language.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code: see at least paragraph 0096 (of the application publication). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 23-25 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to patent eligible subject matter. The instant claims are product claims reciting a 3’-5’ exonuclease enzyme that is not markedly different from naturally occurring 3’-5’ exonuclease enzyme.
Claims 23-25 are directed to a composition (mixture) comprising a 3’-5’ exonuclease enzyme and a buffer. The claims as whole do not recite anything significantly different than the natural product, i.e. the claims do not include elements or features that demonstrate that the recited 3’-5’ exonuclease enzyme is markedly different from what exists in nature. The 3’-5’ exonuclease enzyme is found in nature and in E. coli (see specification). There is no marked and/or significant structural different between the 3’-5’ exonuclease enzyme recited in the instant claims and the 3’-5’ exonuclease enzyme in for instance, E. coli. Although the claims further recite a mix (or composition) and a buffer, the incorporation of protein in a buffer is not only well-understood, routine and conventional activity already engaged in by the scientific community, it is also required for maintaining and using the protein. Additionally, the claims recite the buffer at such a high level of generality that it merely tells a scientist to use any general buffer available. There is no indication of transformation resulting in an altered structure of the 3’-5’ exonuclease enzyme from the naturally occurring 3’-5’ exonuclease enzyme, when placed in any general buffer. Therefore, the claims as a whole add nothing significantly more to the “product of nature” itself. See Funk Brothers Seed Co., V. Kalo Inoculant Co., 333 U.S. 127, (1948) and Association for Molecular Pathology v. Myriad Genetics, Inc. 569 U.S., 133 S. Ct. 2107, 2116, 106 USPQ 2d. 1972 (2013).
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 25 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 25 recites the 3’-5’ exonuclease enzyme XthA is encoded by a nucleic acid sequence of SEQ ID NO: 2. However, it is disclosed in the instant specification that instant SEQ ID NO: 2 is the amino acid sequence of enzyme XthA and instant SEQ ID NO: 1 is the nucleic acid sequence encoding enzyme XthA (paragraphs 0061-0063 of the publication application). Further clarification and/or correction is requested.
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 (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 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.
Claims 23, 26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hou et al. (2015 Analyst 140: 5748-5753). Hou et al. teach a composition or mixture comprising Exo III (exonuclease III), Tris-HCl (pH 7.9, 50 mM NaCl, 10 mM MgCl2, 1mM DTT), and ATP (at least p. 5749-5750). Therefore, Hou et al. can be deemed to anticipate instant claims 23, 26.
Claims 23-25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Saporito et al. (1988 Journal of Bacteriology 170(10): 4542-4547). Saporito et al. teach purification of Exonuclease III from E. coli (p. 4542). Saporito et al. teach a composition or solution comprising the E. coli Exonuclease III, KCl, potassium phosphate, DTT (at least p. 4542). Saporito et al. teach the nucleic acid sequence and amino acid sequence of the E. coli Exonuclease III (at least p. 4545), where the nucleic acid sequence encodes the amino acid sequence of the E. coli Exonuclease III and having 100% sequence identity to instant SEQ ID NO: 1 (the nucleic acid sequence encoding XthA) (see appendix A). Therefore, Saporito et al. can be deemed to anticipate instant claims 23-25.
Claims 23, 26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wen et al. (2015 Anal Methods 7: 3708-3713). Wen et al. teach a composition or mixture comprising Exo III, Tris-HCl, MgCl2, DTT, and ATP (at least p. 3709). Therefore, Wen et al. can be deemed to anticipate instant claims 23, 26.
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.
Claims 23, 26, 27-28 are rejected under 35 U.S.C. 103 as being unpatentable over Hou et al. (2015 Analyst 140: 5748-5753). The teachings of Hou et al. over at least instant claims 23, 26 are noted above.
Regarding instant claims 27-28, Dou et al. disclose concentrations including 10 mM Tris-HCl, 10 mM MgCl2, 1 mM DTT, 50 nM ATP (at least p. 5749-5750). “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to arrive at the recited buffer component concentrations including about 40-60 mM Tris-HCl, about 20-500 mM MgCl2, about 8-12 mM ATP, about 8-12 mM DTT, by routine optimization. One of ordinary skill would have a reasonable expectation of success because the prior art discloses a composition comprising the same buffer components recited at similar concentrations to contain the same enzyme recited.
Claims 23, 26, 27-28 are rejected under 35 U.S.C. 103 as being unpatentable over Wen et al. (2015 Anal Methods 7: 3708-3713). The teachings of Wen et al. over at least instant claims 23, 26 are noted above.
Regarding instant claims 27-28, Wen et al. disclose a 10X Exo III buffer (500 mM Tris-HCl, 50 mM MgCl2, 10 mM DTT, pH 8.0) to prepare compositions comprising Exo III solution and different ATP concentrations 0.05-5 µM (at least p. 3709-3711). “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to arrive at the recited buffer component concentrations including about 40-60 mM Tris-HCl, about 20-500 mM MgCl2, about 8-12 mM ATP, about 8-12 mM DTT, by routine optimization. One of ordinary skill would have a reasonable expectation of success because the prior art discloses a composition comprising the same buffer components recited at similar concentrations to contain the same enzyme recited.
Claims 23, 24-25, 26-28 are rejected under 35 U.S.C. 103 as being unpatentable over Hou et al. (2015 Analyst 140: 5748-5753) or Wen et al. (2015 Anal Methods 7: 3708-3713) in view of Saporito et al. (1988 Journal of Bacteriology 170(10): 4542-4547). The teachings of Hou et al./Wen et al. over at least instant claims 23, 26-28 are noted above. Hou et al./Wen et al. do not explicitly teach the Exo III is an E. coli Exo III.
As noted above, Saporito et al. disclose a purified Exonuclease III from E. coli (p. 4542). Saporito et al. disclose the nucleic acid sequence and amino acid sequence of the E. coli Exonuclease III (at least p. 4545), where the nucleic acid sequence encodes the amino acid sequence of the E. coli Exonuclease III and having 100% sequence identity to instant SEQ ID NO: 1 (the nucleic acid sequence encoding XthA) (see appendix A).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the E. coli Exonuclease III of Saporito et al. for the Exo III in the composition comprising Exo III and buffer of Hou et al./Wen et al. noted above (instant claims 24-25). The motivation to do so is given by the prior art, which disclose that Exo III enzymes known in the art include E. Coli Exonuclease III (XthA). One of ordinary skill would have a reasonable expectation of success because the E. coli Exonuclease III has the same function and/or activity as the Exo III enzyme in Hou et al./Wen et al.
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Marsha Tsay whose telephone number is (571)272-2938. The examiner can normally be reached M-F.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath N. Rao can be reached at 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Marsha Tsay/Primary Examiner, Art Unit 1656
Appendix A
LOCUS X13002 1246 bp DNA linear BCT 23-OCT-2008
DEFINITION E. coli xthA gene for exonuclease III.
ACCESSION X13002
VERSION X13002.1
KEYWORDS exonuclease III; xthA gene.
SOURCE Escherichia coli K-12
ORGANISM Escherichia coli K-12
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
REFERENCE 1 (bases 1 to 1246)
AUTHORS Saporito,S.M., Smith-White,B.J. and Cunningham,R.P.
TITLE Nucleotide sequence of the xth gene of Escherichia coli K-12
JOURNAL J. Bacteriol. 170 (10), 4542-4547 (1988)
PUBMED 3049539
COMMENT see also J. Bacteriology 170:4542-4547(1988).
FEATURES Location/Qualifiers
source 1..1246
/organism="Escherichia coli K-12"
/mol_type="genomic DNA"
/strain="K-12"
/isolate="CS520"
/db_xref="taxon:83333"
/map="38.2\%."
/clone="pLC26-8"
regulatory 82..87
/regulatory_class="minus_35_signal"
regulatory 105..110
/regulatory_class="minus_10_signal"
prim_transcript 160..>1031
regulatory 179..185
/regulatory_class="ribosome_binding_site"
/note="pot. ribosome binding site"
CDS 189..995
/codon_start=1
/transl_table=11
/product="exonuclease III"
/protein_id="CAA31424.1"
/db_xref="GOA:P09030"
/db_xref="InterPro:IPR000097"
/db_xref="InterPro:IPR004808"
/db_xref="InterPro:IPR005135"
/db_xref="InterPro:IPR020847"
/db_xref="InterPro:IPR020848"
/db_xref="PDB:1AKO"
/db_xref="UniProtKB/Swiss-Prot:P09030"
/translation="MKFVSFNINGLRARPHQLEAIVEKHQPDVIGLQETKVHDDMFPL
EEVAKLGYNVFYHGQKGHYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGN
VTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLD
IGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSK
GFDDNRGLRIDLLLASQPLAECCVETGIDYEIRSMEKPSDHAPVWATFRR"
Query Match 100.0%; Score 807; Length 1246;
Best Local Similarity 100.0%;
Matches 807; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGAAATTTGTCTCTTTTAATATCAACGGCCTGCGCGCCAGACCTCACCAGCTTGAAGCC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 189 ATGAAATTTGTCTCTTTTAATATCAACGGCCTGCGCGCCAGACCTCACCAGCTTGAAGCC 248
Qy 61 ATCGTCGAAAAGCACCAACCGGATGTGATTGGCCTGCAGGAGACAAAAGTTCATGACGAT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 249 ATCGTCGAAAAGCACCAACCGGATGTGATTGGCCTGCAGGAGACAAAAGTTCATGACGAT 308
Qy 121 ATGTTTCCGCTCGAAGAGGTGGCGAAGCTCGGCTACAACGTGTTTTATCACGGGCAGAAA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 309 ATGTTTCCGCTCGAAGAGGTGGCGAAGCTCGGCTACAACGTGTTTTATCACGGGCAGAAA 368
Qy 181 GGCCATTATGGCGTGGCGCTGCTGACCAAAGAGACGCCGATTGCCGTGCGTCGCGGCTTT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 369 GGCCATTATGGCGTGGCGCTGCTGACCAAAGAGACGCCGATTGCCGTGCGTCGCGGCTTT 428
Qy 241 CCCGGTGACGACGAAGAGGCGCAGCGGCGGATTATTATGGCGGAAATCCCCTCACTGCTG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 429 CCCGGTGACGACGAAGAGGCGCAGCGGCGGATTATTATGGCGGAAATCCCCTCACTGCTG 488
Qy 301 GGTAATGTCACCGTGATCAACGGTTACTTCCCGCAGGGTGAAAGCCGCGACCATCCGATA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 489 GGTAATGTCACCGTGATCAACGGTTACTTCCCGCAGGGTGAAAGCCGCGACCATCCGATA 548
Qy 361 AAATTCCCGGCAAAAGCGCAGTTTTATCAGAATCTGCAAAACTACCTGGAAACCGAACTC 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 549 AAATTCCCGGCAAAAGCGCAGTTTTATCAGAATCTGCAAAACTACCTGGAAACCGAACTC 608
Qy 421 AAACGTGATAATCCGGTACTGATTATGGGCGATATGAATATCAGCCCTACAGATCTGGAT 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 609 AAACGTGATAATCCGGTACTGATTATGGGCGATATGAATATCAGCCCTACAGATCTGGAT 668
Qy 481 ATCGGCATTGGCGAAGAAAACCGTAAGCGCTGGCTGCGTACCGGTAAATGCTCTTTCCTG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 669 ATCGGCATTGGCGAAGAAAACCGTAAGCGCTGGCTGCGTACCGGTAAATGCTCTTTCCTG 728
Qy 541 CCGGAAGAGCGCGAATGGATGGACAGGCTGATGAGCTGGGGGTTGGTCGATACCTTCCGC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 729 CCGGAAGAGCGCGAATGGATGGACAGGCTGATGAGCTGGGGGTTGGTCGATACCTTCCGC 788
Qy 601 CATGCGAATCCGCAAACAGCAGATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 789 CATGCGAATCCGCAAACAGCAGATCGTTTCTCATGGTTTGATTACCGCTCAAAAGGTTTT 848
Qy 661 GACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGT 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 849 GACGATAACCGTGGTCTGCGCATCGACCTGCTGCTCGCCAGCCAACCGCTGGCAGAATGT 908
Qy 721 TGCGTAGAAACCGGCATCGACTATGAAATCCGCAGCATGGAAAAACCGTCCGATCACGCC 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 909 TGCGTAGAAACCGGCATCGACTATGAAATCCGCAGCATGGAAAAACCGTCCGATCACGCC 968
Qy 781 CCCGTCTGGGCGACCTTCCGCCGCTAA 807
|||||||||||||||||||||||||||
Db 969 CCCGTCTGGGCGACCTTCCGCCGCTAA 995