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 with traverse of group I and SEQ ID NO 5 in the reply filed on 2/24/2026 is acknowledged. The traversal is on the ground(s) that Applicant traverses on the grounds that the generic claim includes sufficiently few species that a search and examination of all the species at one time would not impose a serious burden on the Examiner. This is not found persuasive because searching a DNA polymerase will not inherently provide art on nucleic acids, expression vector, host cells or incorporating modified nucleic acids and vice versa. Thus searching more than one would place a serious search burden on the office.
Claims 102-103, withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 2/24/2026.
Priority
The instant application was filed 09/27/2023 and claims priority from provisional application 63412241 , filed 09/30/2022 and claims priority from provisional application 63433971 , filed 12/20/2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 2/24/2026 is being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 97-98, and 113 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 recites, “An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.”
Dependent claim 98 requires the
Claim 113 is drawn to The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is :the amino acid at position Phe405; the amino acid at position Asn568;the amino acid at position Glu580; the amino acid at position Glu580, and a second substitution mutation is at position Phe405; the amino acid at position Glu580, and a second substitution mutation is at position Val485; the amino acid at position Glu580, and a second substitution mutation is at position Trp516; the amino acid at position Glu580, and a second substitution mutation is at position Leu571; the amino acid at position Glu580, and a second substitution mutation is at position Leu571; the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position I1e410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408;the amino acid at position G1u580, and a second substitution mutation is at position Phe405;the amino acid at position G1u580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Va1485;the amino acid at position Phe405, a second substitution mutation is at position Va1485, and a third substitution mutation is at position A1a408;the amino acid at position Phe405, and a second substitution mutation is at position I1e410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position A1a408, a third substitution mutation is at position I1e410, and a fourth substitution mutation is at position G1y497;the amino acid at position Phe405, a second substitution mutation is at position I1e410, a third substitution mutation is at position I1e412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position I1e521; or the amino acid at position Phe405, a second substitution mutation is at position A1a408, a third substitution mutation is at position I1e410, a fourth substitution mutation is at position I1e412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position I1e521.
Thus the claims encompass any altered archaeal Family B DNA polymerase by any standard.
Further the claims encompass anything which can be considered, “substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1.” Thus the claims are not limited to SEQ ID NO 1, as this is only a reference. Thus the claim encompass an enormous genus of anything which can be considered an archaeal Family B DNA polymerase.
While the specification teaches:
0052] An altered polymerase described herein can be based on the amino acid sequence of a known polymerase (also referred to herein as a reference polymerase) and further includes substitution mutations at one or more residues. In one embodiment, a substitution mutation is at a position functionally equivalent to an amino acid of a reference polymerase. By "functionally equivalent" it is meant that the altered polymerase has the amino acid substitution at the amino acid position in the reference polymerase that has the same functional role in both the reference polymerase and the altered polymerase.
[0053] In general, functionally equivalent substitution mutations in two or more different polymerases occur at homologous amino acid positions in the amino acid sequences of the polymerases. Hence, use herein of the term "functionally equivalent" also encompasses mutations that are "positionally equivalent" or "homologous" to a given mutation, regardless of whether or not the particular function of the mutated amino acid is known. It is possible to identify the locations of functionally equivalent and positionally equivalent amino acid residues in the amino acid sequences of two or more different polymerases on the basis of sequence alignment and/or molecular modelling. An example of sequence alignment to identify positionally equivalent and/or functionally equivalent residues is set forth in FIG. 1. For example, the residues in the Twa, KOD, Pab, Pfu, Deep Vent, and Vent polymerases of FIG. 1 that are vertically aligned are considered positionally equivalent as well as functionally equivalent to the corresponding residue in the 9°N polymerase amino acid sequence. Thus, for example residue 358 of the 9°N, Twa, KOD Pfu, Deep Vent, and Pab polymerases and residue 360 of the Vent polymerase are functionally equivalent and positionally equivalent. Likewise, for example residue 633 of the 9°N, Twa, KOD, and Pab polymerases, residue 634 of the Pfu and Deep Vent polymerases, and residue 636 of the Vent polymerase are functionally equivalent and positionally equivalent. The skilled person can easily identify functionally equivalent residues in DNA polymerases.
The specification teaches:
[0048] In certain embodiments, a family B archaeal DNA polymerase is from a genus such as, for example, Thermococcus, Pyrococcus, Methanococcus, Pyrobaculum, Pyrodictium, and Aeropyrum. Members of the genus Thermococcus are well known in the art and include, but are not limited to T. 4557, T. barophilus, T. gammatolerans, T. onnurineus, T. sibiricus, T. kodakarensis, T. gorgonarius (TGO), and T. waiotapuensis. Members of the genus Pyrococcus are well known in the art and include, but are not limited to P. NA2, P. abyssi, P. furiosus, P. horikoshii, P. yayanosii, P. endeavori, P. glycovorans, and P. woesei. Members of the genus Methanococcus are well known in the art and include, but are not limited to M. aeolicus, M maripaludis, M vannielii, M. voltae, M thermolithotrophicus, and M jannaschii. Members of the genus Pyrobaculum are well known in the art and include, but are not limited to, P. calidifontis (Pc). Members of the genus Pyrodictium are well known in the art and include, but are not limited to, P. occultum. Members of the genus Aeropyrum are well known in the art and include, but are not limited to, A. pernix. [0049] In one embodiment an altered family B DNA polymerase is based on Vent®, Deep Vent®, 9°N, Pfu, KOD, or a Pab polymerase. Vent® and Deep Vent® are commercial names used for family B DNA polymerases isolated from the hyperthermophilic archaeon Thermococcus litoralis. 9°N polymerase is a family B polymerase isolated from Thermococcus sp. 9°N-7. Pfu polymerase is a family B polymerase isolated from Pyrococcusfuriosus. KOD polymerase is a family B polymerase isolated from Thermococcus kodakarensis. Pab polymerase is a family B polymerase isolated from Pyrococcus abyssi. Twa is a family B polymerase isolated from T. waiotapuensis. Examples of Vent®, Deep Vent®, 9°N, Pfu, KOD, Pab, and Twa polymerases are disclosed in Figure 1.
Makarova (frontiers in Microbiology (2014) volume 5) teaches there are 3 members of the archaeal family B DNA polymerases. Makarova teaches, “ Family B DNAPs are present in all archaeal lineages, and many archaea have multiple paralogs some of which appear to be inactivated; at least two paralogs can be traced to the Last Archaeal Common Ancestor (LACA) (Rogozin et al., 2008; Makarova and Koonin, 2013). In addition to the archaeal chromosomes, family B DNAPs are encoded by several mobile genetic elements (MGEs) that replicate in archaeal cells and could contribute to horizontal transfer of DNAPs (Filee et al., 2002). In particular, family B DNAPs closely related to those found in the host species are encoded by haloarchaeal head-tailed viruses such as Halorubrum myoviruses HF1, HF2 (Filee et al., 2002; Tang
et al., 2002) and HSTV-2 (Pietila et al., 2013) whereas more diverged protein-primed Family B DNAPs have been identified in other haloviruses such as His1 and His2 (Bath et al., 2006). Furthermore, recently, family B DNAPs have been identified in a new group of self-synthesizing mobile elements, called casposons because they apparently employ Cas1, originally known as a component of the CRISPR-Cas immunity systems, as their integrase (Makarova et al., 2013; Krupovic et al., 2014a)” (2nd column page 1-page 2).
Further the specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least
99% amino acid sequence identity to the reference polymerase.”
Rafiq (Biology 2023, 12, 1499.) teaches, “an estimated number of archaeal phyla in the SILVA database based on ribosomal small unit gene sequencing is 30, containing 20,000 species [24,25]. At the same time, the taxonomic classification based on the genome at the Genome Taxonomy Database (GTDB) has 21 phyla with 7777 species.”
Thus the claims encompass an enormous genus of archaeal Family B DNA polymerases as there is generally 3 family members in each species and between 7777 and 20000 species of archaeal. This is an enormous genus.
Further the claims require,” the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.” Thus the claims encompass 2 functional outcomes relative to SEQ ID NO 1 under any conditions such as pH, nucleotide concentration, temperature, etc. Further dependent claims require, “The altered archaeal Family B DNA polymerase of claim 1, wherein the polymerase comprises reduced exonuclease activity as compared to SEQ ID NO:9.” However the specification provides no structure function relationship. Further review of the specification did not appear to provide any data supporting the mutations of SEQ ID NO of the claim and the claimed functional outcome
Thus while the claims encompass an enormous genus of altered archaeal group B DNA polymerase. The claims lack adequate written description.
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, 98, and 113 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, “capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.” The recitation of capable of incorporating suggests there is incapable of incorporating a modified nucleotide. The specification does not provide a standard to differentiate the two. Further the metes and bounds are unclear as while the claim recites, “(i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.” The metes and bounds are unclear under what conditions the lower error rate and/or lower phasing rate is relative to and under what conditions. Thus the metes and bounds are unclear what structure provides for these intended outcomes.
Further claim 1 recites, “wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1.” While the specification teaches: By "functionally equivalent" it is meant that the altered polymerase has the amino acid substitution at the amino acid position in the reference polymerase that has the same functional role in both the reference polymerase and the altered polymerase.” The metes and bounds are unclear as the definition is circular as it relies upon the relative term of “the same functional role.” Thus the metes and bounds are unclear.
Claim 113 recites “the altered archaeal Family B DNA polymerase.” This limitation lacks antecedent basis as the claim does not previously recite,” altered archaeal Family B DNA polymerase.” This rejection can be overcome by amending the claim to depend from claim 1.
Further claim 113 recites multiple amino acid positions. However, the claim does not recite a SEQ ID NO. Thus the metes and bounds are unclear what the positions are relative to.
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 1, 97-98, and 113 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an altered archaeal Family B DNA polymerase. The claim(s) encompass naturally occurring altered archaeal Family B DNA polymerase . This judicial exception is not integrated into a practical application because if there is no requirement demonstrating the hand of man. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claim encompass naturally occurring archaeal Family B DNA polymerase.
Claim analysis
The instant claim 1 is directed towards “An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.”
Claim 113 is directed toward” The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is :the amino acid at position Phe405; the amino acid at position Asn568;the amino acid at position Glu580; the amino acid at position Glu580, and a second substitution mutation is at position Phe405; the amino acid at position Glu580, and a second substitution mutation is at position Val485; the amino acid at position Glu580, and a second substitution mutation is at position Trp516; the amino acid at position Glu580, and a second substitution mutation is at position Leu571; the amino acid at position Glu580, and a second substitution mutation is at position Leu571; the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position I1e410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408;the amino acid at position G1u580, and a second substitution mutation is at position Phe405;the amino acid at position G1u580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Va1485;the amino acid at position Phe405, a second substitution mutation is at position Va1485, and a third substitution mutation is at position A1a408;the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position A1a408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position G1y497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position A1a408, a third substitution mutation is at position I1e410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.”
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least
99% amino acid sequence identity to the reference polymerase.”
While the claims recite altered, the claims encompass naturally occurring archaeal family B DNA polymerases. The claims provides no specific limitation demonstrating the hand of man.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a composition.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, they are drawn to a natural composition or natural phenomenon.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as the claim provide no limitations which demonstrate the archaeal family B DNA polymerase encompassed is not naturally occurring..
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No, the claims provide no specific limitations requiring the hand of man.
DNA polymerase [Thermococcus peptonophilus] (WP_062388189.1) March 26, 2016 (https://www.ncbi.nlm.nih.gov/protein/1011493512?sat=48&satkey=68279833) demonstrates the sequence encompasses naturally occurring DNA polymerases with more than 65% identity with the claimed SEQ ID NO. Thus the claims are non-statutory of 101.
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.
(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.
Claim(s) 1, 97, 98, 113 is/are rejected under 35 U.S.C. 102(a)(1)/102(s)(2) as being anticipated by Miller (US Patent 11,060,075).
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
SEQ ID NO 6 (sbjct) of Miller has 99% identity with instantly claimed SEQ ID NO 5.(query)
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AS presented the claims appear to require the archaeal DNA polymerases with the claimed structure amino acid sequence provide for the intended outcomes of the claims and thus anticipates claims 1, 97,98 and 113)
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. 12,110,514. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497; the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 514 are drawn to An altered family B archaeal polymerase comprising an amino acid sequence that is at least 90% identical to SEQ ID NO:10, wherein the altered polymerase comprises amino acid substitution mutations at the positions functionally equivalent to Lys477 and Ala485 in the wild-type 9°N DNA polymerase amino acid sequence of SEQ ID NO:5.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 10,870,836. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 836 are drawn to an altered family B archaeal polymerase comprising at least one amino acid substitution mutation at the position functionally equivalent to Lys477 in the wild-type 9° N DNA polymerase amino acid sequence of SEQ ID NO:5, wherein the substitution mutation is homologous to Lys477Met, and wherein the altered polymerase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO:10, and wherein the altered polymerase further comprises substitution mutations at one or more positions functionally equivalent to Asp141 and/or Glu143 in the 9° N DNA polymerase amino acid sequence..
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 9,765,309. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position G1u580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 309 are drawn to an altered family B archaeal DNA polymerase comprising-amino acid substitution mutations at the positions functionally equivalent to Leu408, Tyr409, Pro410, and Lys477 in the wild-type 9° N DNA polymerase amino acid sequence of SEQ ID NO:5, wherein the substitution mutations are homologous to Leu408Ala, Tyr409Ala, Pro410Ile, and Lys477Met, wherein the altered polymerase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO:11.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 10,745,751. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 751 are drawn to A DNA polymerase comprising the amino acid sequence of SEQ ID NO: 30..
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 10,421,996. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position G1u580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position G1y497; the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 996 are drawn to A DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs: 32-34..
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-29 of U.S. Patent No. 11,198,854. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position G1y497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 854 are drawn to A recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to SEQ ID NO: 10, which recombinant DNA polymerase comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Thr144, Gly153, Lys476, Leu478, Thr590, Ala639 or Asp718 in the 9° N DNA polymerase amino acid sequence, wherein the mutation at the position functionally equivalent to Gly153 comprises a mutation to a polar amino acid, wherein the mutation at the position functionally equivalent to Lys476 comprises a mutation to a hydrophobic amino acid, wherein the mutation at the position functionally equivalent to Lys478 comprises a mutation to a polar amino acid, and which recombinant DNA polymerase further comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Leu408, Tyr409, Pro410, or a combination thereof, in the 9° N DNA polymerase amino acid sequence, and wherein the DNA polymerase is a family B DNA polymerase...
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. 10,696,955. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 955 are drawn A method for incorporating modified nucleotides into DNA comprising allowing the following components to interact: (i) a DNA template; (ii) a nucleotide solution; and (iii) a recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to SEQ ID NO:10, which recombinant DNA polymerase comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Thr144, Gly153, Lys476, Leu478, Thr590, Ala639 or Asp718 in the 9° N DNA polymerase amino acid sequence, wherein the mutation at the position functionally equivalent to Gly153 comprises a mutation to a polar amino acid, wherein the mutation at the position functionally equivalent to Lys476 comprises a mutation to a hydrophobic amino acid, wherein the mutation at the position functionally equivalent to Leu478 comprises a mutation to a polar amino acid, wherein the mutation at the position functionally equivalent to Asp718 comprises a mutation homologous to Asp718Asn, and wherein the DNA polymerase is a family B DNA polymerase....
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-38 of U.S. Patent No. 10,150,954. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 954 are drawn A recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to SEQ ID NO: 10, which recombinant DNA polymerase comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Thr144, Gly153, Lys476, Leu478, Thr590, Ala639 or Asp718 in the 9° N DNA polymerase amino acid sequence, wherein the mutation at the position functionally equivalent to Lys476 comprises a mutation to a hydrophobic amino acid, wherein the mutation at the position functionally equivalent to Lys478 comprises a mutation to a polar amino acid, wherein the mutation at the position functionally equivalent to Gly153 comprises a mutation to a polar amino acid, and which recombinant DNA polymerase further comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Cys223, Thr514, Lys477, or Ile521 in the 9° N DNA polymerase amino acid sequence, and wherein the DNA polymerase is a family B DNA polymerase..
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. 9,677,057. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485; the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position G1u580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 057 are drawn A recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to SEQ ID NO:10, which recombinant DNA polymerase comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Thr144, Gly153, Lys476, Leu478, Thr590, Ala639 or Asp718 in the 9° N DNA polymerase amino acid sequence, wherein the mutation at the position functionally equivalent to Gly153 comprises a mutation to a polar amino acid, wherein the mutation at the position functionally equivalent to Lys476 comprises a mutation to a hydrophobic amino acid, wherein the mutation at the position functionally equivalent to Leu478 comprises a mutation to a polar amino acid, wherein the mutation at the position functionally equivalent to Asp718 comprises a mutation homologous to Asp718Asn, and wherein the DNA polymerase is a family B DNA polymerase...
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 10,995,324. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568; the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position G1u580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 324 are drawn A nucleic acid molecule encoding a recombinant DNA polymerase, the recombinant DNA polymerase comprising an amino acid sequence that is at least 95% identical to SEQ ID NO:14, and which recombinant DNA polymerase exhibits polymerase activity...
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 10,329,545. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position G1u580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position I1e410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 545 are drawn A recombinant DNA polymerase comprising the amino acid sequence of SEQ ID NO: 14.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-31 of U.S. Patent No. 11,104,888. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 888 are drawn A recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to the 9° N DNA polymerase amino acid sequence SEQ ID NO:1, wherein the recombinant DNA polymerase comprises an amino acid substitution mutation at a position functionally equivalent to Tyr497 and at least one amino acid substitution mutation at a position functionally equivalent to Phe152, Val278, Met329, Val471, Thr514, Leu631, or Glu734 in the 9° N DNA polymerase amino acid sequence, wherein the amino acid substitution mutation at a position functionally equivalent to Tyr497 comprises a mutation to Gly, Ile, Leu, Met, Pro, Val, Ser, Asn, Gln, or Thr.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-38 of U.S. Patent No. 11,560,552. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 552 are drawn A nucleic acid molecule encoding a recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to the 9° N DNA polymerase amino acid sequence SEQ ID NO:1, wherein the recombinant DNA polymerase comprises an amino acid substitution mutation at a position functionally equivalent to Tyr497 and at least one amino acid substitution mutation at a position functionally equivalent to Phe152, Val278, Met329, Val471, Thr514, Lys620, Leu631, Val661 or Glu734 in the 9° N DNA polymerase amino acid sequence, wherein the amino acid substitution mutation at a position functionally equivalent to Tyr497 comprises a mutation to Gly, Ile, Leu, Met, Pro, Val, Ser, Asn, Gln, or Thr.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 97, 98, 113 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-33 of U.S. Patent No. 12,077,789. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
An altered archaeal Family B DNA polymerase comprising the amino acid sequence of any one of SEQ ID NOs:2-8 or any one of SEQ ID NOs:16-32.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568; the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position Gly497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 789 are drawn A recombinant family B archaeal DNA polymerase comprising an amino acid sequence that is at least 80% identical to a DNA polymerase amino acid sequence SEQ ID NO:8 or 12, wherein the recombinant DNA polymerase comprises at least two substitution mutations, wherein the first substitution mutation at the position functionally equivalent to Ala408 comprises a mutation to Tyr, and wherein the second substitution mutation at the position functionally equivalent to Ala409 comprises a mutation to Pro, and wherein the recombinant DNA polymerase preferentially incorporates a nucleotide having a blocking group at a faster rate than a nucleotide lacking the blocking group..
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Claim 1, 97, 98, 113 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1, 3, 5, 7, 11, 14-15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41 of copending Application No. 18/824,208. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to An altered archaeal Family B DNA polymerase, wherein the altered archaeal Family B DNA polymerase comprises at least one amino acid substitution mutation at a position functionally equivalent to an amino acid in a reference archaeal Family B DNA polymerase of SEQ ID NO: 1, and the altered archaeal Family B DNA polymerase is capable of incorporating a modified nucleotide comprising a 3'-OH acetal blocking group or a 3'- OH thiocarbamate blocking group at (i) a lower error rate, (ii) a lower phasing rate, or both (i) and (ii), compared to SEQ ID NO: 1.
The altered archaeal Family B DNA polymerase, wherein the at least one amino acid substitution mutation is: the amino acid at position Phe405;the amino acid at position Asn568;the amino acid at position Glu580;the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Val485;the amino acid at position Glu580, and a second substitution mutation is at position Trp516;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, and a second substitution mutation is at position Leu571;the amino acid at position Glu580, a second substitution mutation is at position Ala408, and a third mutation is at position Ile410;the amino acid at position Glu580, and a second substitution mutation is at position Ala408; the amino acid at position Glu580, and a second substitution mutation is at position Phe405;the amino acid at position Glu580, and a second substitution mutation is at position Ile410;the amino acid at position Phe405, and a second substitution mutation is at position Val485;the amino acid at position Phe405, a second substitution mutation is at position Val485, and a third substitution mutation is at position Ala408; the amino acid at position Phe405, and a second substitution mutation is at position Ile410;the amino acid at position Phe140, and a second substitution mutation is at position Ser407;the amino acid at position Leu403, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, and a fourth substitution mutation is at position G1y497;the amino acid at position Phe405, a second substitution mutation is at position Ile410, a third substitution mutation is at position Ile412, a fourth substitution mutation is at position Thr514, and a fifth substitution mutation is at position Ile521; or the amino acid at position Phe405, a second substitution mutation is at position Ala408, a third substitution mutation is at position Ile410, a fourth substitution mutation is at position Ile412, a fifth substitution mutation is at position Thr514, and a sixth substitution mutation is at position Ile521.
The specification teaches, “[0065] Thus, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence similarity to the reference polymerase. [0066] Alternatively, as used herein, reference to a polymerase as described herein, such as reference to the amino acid sequence of one or more SEQ ID NOs described herein can include a protein with at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the reference polymerase.”
The claims of 208 are drawn A recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to a polymerase amino acid sequence SEQ ID NO:4, SEQ ID NO:5, or SEQ ID NO:6, wherein the DNA polymerase comprises an amino acid substitution mutation at a position functionally equivalent to Ala281, Phe283, Thr349, or Trp397 in the 9°N DNA polymerase amino acid sequence SEQ ID NO:1..
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the patent encompass the instant DNA polymerases of the claims in view of the teachings of the specification.
Dependent claims are obvious as they are coextensive in scope.
Summary
No claims are allowed.
Conclusion
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/Steven Pohnert/Primary Examiner, Art Unit 1683
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