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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/19/2025 has been entered.
Applicant’s amendment of claims 31, 61, 62 in the paper of 12/19/2025, is acknowledged. Applicants' arguments filed on 12/19/2025, have been fully considered and are deemed to be persuasive to overcome some of the rejections previously applied. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. Claims 31-33, 57-64 are still at issue and are present for examination.
Election/Restriction
Applicant’s election of Group 3, claims 31, 32, 33 and 49, drawn to a method of controlling movement of a polynucleotide, in the paper of 1/17/2025, is acknowledged.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 31-33, 57-64 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 pre-AIA the applicant regards as the invention.
Claim 31 (claims 32-33, 57-64 dependent on) is indefinite in the recitation “an amino acid that increases interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide;” in that this recitation and description of the referred to amino acid substitution is confusing and unclear. Previously the claim was rejected for the recitation “an amino acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide;” was indefinite. Specifically the previous recitation was indefinite with regard to “improves” as it is unclear what improves is in the context of the claim. While it was recognized that improves is a relative term, it was further unclear what an amino acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide is because it is unclear what improves is. Applicants in response have amended the claims from “improves interaction” to “increases interaction” and traverse the rejection based upon this amendment.
Applicants amendment of the claims and applicants complete traversal is acknowledged and has been carefully considered, however, is not found persuasive for the reasons stated previously and for those reasons repeated herein.
The claim remains indefinite in the recitation “an amino acid that increases interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide;” in that this recitation and description of the referred to amino acid substitution is confusing and unclear for the same reasons previously stated for the recitation “an amino acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide;”. Specifically the recitation is indefinite with regard to “increases” as it is unclear what increases is in the context of the claim. While it was recognized that increases is a relative term, it is further unclear what an amino acid that increases interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide is because it is unclear what increases interaction is. It is noted that applicants specification does not clarify the above, however, applicants specification does state “[0132] The substitution preferably increases the (i) electrostatic interactions, (ii) hydrogen bonding and/or (iii) cation-pi (cation-π) interactions between the at least one amino acid and the one or more phosphate groups in ssDNA.” which may help applicants overcome the rejection.
The rejection of claim 31 (claims 32-33, 57-64 dependent on) as indefinite in the recitation “a motif selected from: motif Ia, motif Ic, motif III, motif IV, motif V, and motif Vb” is withdrawn based upon applicants arguments filed in the paper of 19/19/2025 and the supporting Declaration under 37 CFR 1.132 by Rebecca Bowen.
Previously, claim 31 (claims 32-33, 57-64 dependent on) was indefinite in the newly added recitation “wherein the positions are numbered by alignment of the amino acid sequence of the Dda helicase to the amino acid sequence set forth in SEQ ID NO: 8” as it is unclear and confusing as to applicants intended meaning. Applicants specification teaches that with regard to that part which interacts with the pore, positions 1-6, 51, 176-181, 185, 189, 191, 193-204,207-213,216,219-221,223,224,226-229,247,254-261, 298, 300, 304, 308, 318, 319, 321, 337, 347, 350, 351, 405, 415, 422, 434, 437 and 438 are relevant to SEQ ID NO:8. This does not appear to be the same as the recitation “wherein the positions are numbered by alignment of the amino acid sequence of the Dda helicase to the amino acid sequence set forth in SEQ ID NO: 8” and as such the recitation is indefinite.
Applicants traverse this rejection on the basis that applicants submit that one of skill in the art would understand that the positions are relative and thus relevant to any Dda helicase amino acid sequence if interest. Applicants submit that sequence alignment tools are commonly used by those of ordinary skill in the art. In making applicants argument applicants state “while the positions recited in claim 31 are numbered according to SEQ ID NO: 8, one of ordinary skill in the art would understand that these positions can also be used to refer to corresponding positions in other Dda helicases, so long as the amino acid sequences are aligned”.
Applicants argument is not found persuasive for the reasons previously made of record and repeated above.
While it is understood that the positions are relative and relevant to any Dda helicase amino acid sequence, they must be relative to a sequence to which the “any Dda helicase amino acid sequence” may be aligned. Applicants even state in their argument that “the positions recited in claim 31 are numbered according to SEQ ID NO: 8”. This was similarly stated in the previous office action. Just because “the positions recited in claim 31 are numbered according to SEQ ID NO: 8, does not preclude those defined positions in the context of other amino acid sequences based upon their alignment to SEQ ID NO:8. The rejection is not based upon what is encompassed by the rejected language in the context of the claim but rather the indefiniteness of applicants language in defining the positions to be substituted. The rejection remains for the reasons stated previously and repeated herein.
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.
Claim(s) 31-33 and 57-64 are rejected under 35 U.S.C. 112, first paragraph, as containing 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(s), at the time the application was filed, had possession of the claimed invention.
Claim 31 (claims 32-33, 57-64 dependent on) remains rejected under this statute because the newly added recitation “in a motif selected from: motif Ia, motif Ic, motif III, motif IV, motif V, and motif Vb” is not supported by applicants specification at the time of filing and is thus considered new matter.
It is noted that applicants appear to argue this rejection together with the rejection below based on new matter and the rejection below based upon a lack of written description. It is noted that applicants do not specifically traverse this rejection based upon new matter for the “in a motif selected from: motif Ia, motif Ic, motif III, motif IV, motif V, and motif Vb”.
Newly amended claim 31 (claims 32-33, 57-64 dependent on) is rejected under this statute because the newly added recitation “an amino acid that increases interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide” is not supported by applicants specification at the time of filing and is thus considered new matter.
It is noted that applicants appear to argue this rejection together with the rejection above based on new matter and the rejection below based upon a lack of written description. It is noted that applicants do not specifically traverse this rejection based upon new matter for the “an amino acid that increases interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide”.
Claim(s) 31-33 and 57-64 are rejected under 35 U.S.C. 112, first paragraph, as containing 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(s), at the time the application was filed, had possession of the claimed invention.
This rejection was stated in the previous office action as it applied to previous claims 31-33 and 57-64. In response applicants have amended the claims and argue the rejection as it applies to the newly amended claims.
Newly amended claim(s) 31-33 and 57-64 are directed to all possible methods of controlling the movement of a polynucleotide, comprising: contacting the polynucleotide with a DNA-dependent ATPase (Dda) helicase comprising: (a) at least one substitution of an amino acid that the Dda helicase to the amino acid sequence set forth in SEQ ID NO: 8; wherein the helicase is configured to control the movement of a polynucleotide and (c) controlling the movement of the polynucleotide using the helicase (see also above rejection under 35 U.S.C. 112(b) and 35 U.S.C. 112 (pre-AIA ), second paragraph).
Applicants Response
In response to the above previous rejection, applicants note that they have amended the claims and continue to traverse the rejection as it applies to the newly amended claims. Applicants further submit as evidenced by the Declaration one of ordinary skill in the art would have recognized that the nucleic acid binding function of Dda helicases required by the claimed method was correlated to the structure of Dda helicase domains and motifs and one of ordinary skill would have understood the inventors to have possession of the full genus of variant Dda helicases and methods using.
Applicants traverse the rejection as it applies to the newly amended claims on the following basis. After a review of the requirements of written description, applicants submit that one of ordinary skill in the art would have recognized that the inventors were in possession of the claimed invention because structural and functional characteristics that identify Dda helicases, domains thereof, and combinations thereof as recited in the instant claims were described in the instant specification and known in the art at the time of filing.
Applicants continue to submit that the instant disclosure describes structures characteristic of and correlated to certain functions of Dda helicases, including polynucleotide binding domains and amino acids comprised therein that bind to nucleotides of single stranded polynucleotides, as well as methods of identifying the same in other helicases. Applicants continue to submit that domains of Dda helicases, including 1A and 2A domains, are described in detail in the instant specification, and examples of amino acids within the same domains that interact with nucleotides are also provided". Applicants continue to submit that the structure and polynucleotide binding functions of the 1A and 2A domains in Dda helicases, and polynucleotide binding motifs therein, such as motif Ia (corresponding to positions 61-67 of SEQ ID NO: 8), motif Ic (corresponding to positions 80-84 of SEQ ID NO: 8), motif III (corresponding to positions 142-149 of SEQ ID NO: 8), motif IV (corresponding to positions 236-243 of SEQ ID NO: 8), motif V (corresponding to positions 392- 397 of SEQ ID NO: 8), and motif Vb (corresponding to positions 413-419 of SEQ ID NO: 8), were known by those of ordinary skill in the art before the time of filing, and recognized as sharing a high degree of homology12,13,14,15. Applicants continue to submit that the instant disclosure also provides teachings regarding protein modeling and use of the same for identification of amino acids that interact with nucleotides (e.g., single stranded polynucleotides) within and outside of these polynucleotide binding domains in various homologous helicases1617. Applicants continue to submit that the working examples provide simulation data demonstrating that these regions and specific positions are predicted to have a similar function in various helicases, e.g., as shown in Tables 13 and 14 (pages 111-114 of the instant specification as filed) and as summarized in Table 3 (page 21 of the instant specification as filed). Applicants submit that finally, the instant specification provides teachings regarding certain substitutions of these amino acids, e.g. larger R groups, modifications related to phosphate interactions, and combinations thereof.
Applicants submit that thus, the instant specification provides sufficient detail to reasonably convey to one of skill in the art that the inventors had possession of the recited genus of Dda helicases comprising "substituted amino acids that interact with one or more nucleotides in a single stranded polynucleotide" at the time the application was filed.
Applicants amendment of the claims and applicants complete argument is acknowledged and has been carefully considered, however, is found non-persuasive for the reasons previously stated and for those reasons repeated herein.
In response to applicants submission that the instant disclosure describes structures characteristic of and correlated to certain functions of Dda helicases, including polynucleotide binding domains and amino acids comprised therein that bind to nucleotides of single stranded polynucleotides, while this is acknowledged, applicants are reminded that the current claims rejected under written description are not directed to Dda helicases themselves but rather methods of using Dda helicase mutants to control the movement of a polynucleotide, wherein said Dda helicase comprises a substitutions within defined as well as undefined regions of the Dda polypeptide. In response to applicants submission that domains of Dda helicases, including 1A and 2A domains, are described in detail in the instant specification, this is not persuasive in overcoming the rejection of those methods of controlling the movement of a polynucleotide using the referenced Dda mutants because while applicants specification does identify where within certain amino acid sequences of some Ddas, the domains 1A and 2A occur, applicants specification does not describe the actual structure of the two domains and thus this is insufficient to describe the breadth of the referred to Ddas and their methods of use. In response to applicants submission that the structure and polynucleotide binding functions of the 1A and 2A domains in Dda helicases, and polynucleotide binding motifs therein, such as motif Ia (corresponding to positions 61-67 of SEQ ID NO: 8), motif Ic (corresponding to positions 80-84 of SEQ ID NO: 8), motif III (corresponding to positions 142-149 of SEQ ID NO: 8), motif IV (corresponding to positions 236-243 of SEQ ID NO: 8), motif V (corresponding to positions 392- 397 of SEQ ID NO: 8), and motif Vb (corresponding to positions 413-419 of SEQ ID NO: 8), were known by those of ordinary skill in the art before the time of filing, and recognized as sharing a high degree of homology is not found persuasive on the basis that as stated above, each of the referred to motifs is not supported by applicants original disclosure and are insufficient to describe the claimed methods of controlling the movement of a polynucleotide with a mutant Dda comprising at least one substituted amino acid is in a motif selected from: motif Ia, motif Ic, motif III, motif IV, motif V, and motif Vb; and/or at any one of positions 88, 89, 98, 121, 150, 152, 276, and 287, with an amino acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide and one or more modifications in a domain that interacts with a transmembrane pore, wherein the domain comprises amino acids at positions 1-6, … …438, wherein the positions are numbered by alignment of the amino acid sequence of the Dda helicase to the amino acid sequence set forth in SEQ ID NO: 8.
In response to applicants submission that the working examples provide simulation data demonstrating that these regions and specific positions are predicted to have a similar function in various helicases, while such is helpful, the referred to data and analysis is insufficient to describe claimed breadth of the claimed methods of controlling the movement of a polynucleotide with a mutant Dda comprising at least one substituted amino acid is in a motif selected from: motif Ia, motif Ic, motif III, motif IV, motif V, and motif Vb; and/or at any one of positions 88, 89, 98, 121, 150, 152, 276, and 287, with an amino acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide and one or more modifications in a domain that interacts with a transmembrane pore, wherein the domain comprises amino acids at positions 1-6, … …438, wherein the positions are numbered by alignment of the amino acid sequence of the Dda helicase to the amino acid sequence set forth in SEQ ID NO: 8.
It continues that the specification, however, only provides the representative species of that method of controlling the movement of/characterizing a polynucleotide, comprising: (a) contacting the target polynucleotide with a transmembrane pore and a helicase such that the helicase controls the movement of the target polynucleotide through the pore; and (b) taking one or more electrical measurements as the polynucleotide moves with respect to the pore wherein the measurements are indicative of one or more characteristics of the target polynucleotide and thereby characterizing the target polynucleotide, wherein the helicase is a DNA-dependent ATPase (Dda) helicase in which: (i) at least one amino acid which interacts with one or more nucleotides in single stranded DNA (ssDNA) is recombinantly substituted; and (ii) the part of the Dda helicase which interacts with the transmembrane pore comprises one or more modification, wherein the DNA-dependent ATPase (Dda) helicases comprises the amino acid sequence of SEQ ID NO:8, in which at least one amino acid selected from H82, N88, P89, F98, D121, V150, P152, F240, F276, S287, H396 and Y415 which interacts with one or more nucleotides in single stranded DNA (ssDNA) is substituted; and the part of the helicase which interacts with a transmembrane pore comprises one or more modifications at positions 1-6, 51, 176-181, 185, 189, 191, 193-204, 207-213, 216, 219-221, 223, 224, 226-229, 247, 254-261, 298, 300, 304, 308, 318, 319, 321, 337, 347, 350, 351, 405, 415, 422, 434, 437 and 438, encompassed by these claims. There is no disclosure of any particular structure to function/activity relationship in the disclosed species. The specification also fails to describe additional representative species of these controlling the movement of a polynucleotide with a mutant Dda comprising at least one substituted amino acid is in a motif selected from: motif Ia, motif Ic, motif III, motif IV, motif V, and motif Vb; and/or at any one of positions 88, 89, 98, 121, 150, 152, 276, and 287, with an amino acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide and one or more modifications in a domain that interacts with a transmembrane pore, wherein the domain comprises amino acids at positions 1-6, … …438, wherein the positions are numbered by alignment of the amino acid sequence of the Dda helicase to the amino acid sequence set forth in SEQ ID NO: 8, for which no insufficient predictability of structure/function is apparent. Given this lack of additional representative species as encompassed by the claims, Applicants have failed to sufficiently describe the claimed invention, in such full, clear, concise, and exact terms that a skilled artisan would recognize Applicants were in possession of the claimed invention.
Applicant is referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Claim Rejections - 35 USC § 102
The rejection of claim(s) 31-33 and 49 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Heron et al. (WO 2014/135838) is withdrawn based upon applicants amendment of the claims in the paper of 7/25/2025.
The rejection of claim(s) 31-33 and 49 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jayasinghe et al (WO 2010/004265 published Jan. 14, 2010) is withdrawn based upon applicants amendment of the claims in the paper of 7/25/2025.
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 §§ 706.02(l)(1) - 706.02(l)(3) 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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
Claims 31-33 and 57-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-22 of US 11,965,183. Although the claims at issue are not identical, they are not patentably distinct from each other claims 1-22 of US 11,965,183 are drawn to a method of characterizing a target polynucleotide, comprising: (a) contacting the target polynucleotide with a transmembrane pore and a helicase such that the helicase controls the movement of the target polynucleotide through the pore; and (b) taking one or more electrical measurements as the polynucleotide moves with respect to the pore wherein the measurements are indicative of one or more characteristics of the target polynucleotide and thereby characterizing the target polynucleotide, wherein the helicase is a DNA-dependent ATPase (Dda) helicase in which: (i) the Dda helicase comprises a sequence that is at least 70% identical to the sequence set forth in SEQ ID NO: 8 and is recombinantly substituted in at least one residue corresponding to at least one of the following amino acid positions in SEQ ID NO: 8 which interacts with one or more nucleotides in single stranded DNA (ssDNA): H82, N88, P89, F98, D121, V150, P152, F240, F276, S287, H396 and/or Y415; and (ii) the part of the Dda helicase which interacts with the transmembrane pore comprises one or more modifications at one or more residues corresponding to a position in SEQ ID NO: 8 selected from the group consisting of: 3, 4, 5, 176, 177, 179, 180, 185, 193, 194, 195, 198, 199, 200, 202, 203, 204, 207, 208, 209, 210, 211, 212, 213, 216, 221, 224, 255, 318, 347, 405, 415, 434, 437, and 438. anticipate and make obvious instant claims 31-33 and 57-64 drawn to a method of controlling the movement of a polynucleotide, comprising: contacting the polynucleotide with a DNA-dependent ATPase (Dda) helicase comprising: (a) at least one substitution of an amino acid that
Applicants request for reconsideration of the above rejections based upon claim amendments presented herein is acknowledged, however, is not found persuasive in overcoming the rejection for the reasons stated above.
Claims 31-33 and 57-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5 of US 10,724,018. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-5 of US 10,724,018 are drawn to method of controlling the movement of a polynucleotide with respect to a transmembrane pore, comprising contacting the polynucleotide with a DNA-dependent ATPase (Dda) helicase modified to comprise a first cysteine residue and/or a first non-natural amino acid that has been introduced into (i) the tower domain, (ii) the pin domain, or (iii) the 1A (RecA-like motor) domain, wherein the first cysteine residue and/or the first non-natural amino acid is connected to a second cysteine residue and/or second non-natural amino acid that has been introduced into (i) the tower domain, (ii) the pin domain, or (iii) the 1A (RecA-like motor) domain and wherein the helicase retains its ability to control the movement of a polynucleotide with respect to the transmembrane pore, and thereby controlling the movement of the polynucleotide, in order to form a complex; and contacting a transmembrane pore with the complex anticipate and make obvious instant claims 31-33 and 57-64 drawn to a method of controlling the movement of a polynucleotide, comprising: contacting the polynucleotide with a DNA-dependent ATPase (Dda) helicase comprising: (a) at least one substitution of an amino acid that acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide; and (b)
Applicants request for reconsideration of the above rejections based upon claim amendments presented herein is acknowledged, however, is not found persuasive in overcoming the rejection for the reasons stated above.
Claims 31-33 and 57-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of US 10,443,097. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-10 of US 10,443,097 are drawn to method of characterizing a target polynucleotide, comprising: a) providing a transmembrane pore and a polynucleotide binding protein in which a part of the transmembrane pore which interacts with the polynucleotide binding protein and/or a part of the polynucleotide binding protein which interacts with the transmembrane pore has been modified, wherein the modification comprises an amino acid substitution, insertion, or deletion relative to an unmodified transmembrane pore or polynucleotide binding protein; b) contacting the transmembrane pore and polynucleotide binding protein provided in (a) with the target polynucleotide such that the polynucleotide binding protein controls the movement of the polynucleotide with respect to the transmembrane pore; and c) taking one or more electrical or optical measurements as the polynucleotide moves with respect to the transmembrane pore anticipate and make obvious instant claims 31-33 and 57-64 drawn to a method of use or a method of controlling the movement of a polynucleotide, comprising: contacting the polynucleotide with a DNA-dependent ATPase (Dda) helicase comprising: (a) at least one substitution of an amino acid that ID NO: 8; wherein the helicase is configured to control the movement of a polynucleotide; thereby controlling the movement of the polynucleotide.
Applicants request for reconsideration of the above rejections based upon claim amendments presented herein is acknowledged, however, is not found persuasive in overcoming the rejection for the reasons stated above.
Claims 31-33 and 57-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of US 10,724,087. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-13 of US 10,724,087 are drawn to method of characterizing a target polynucleotide, comprising: (a) contacting the target polynucleotide with a transmembrane pore, wherein a first helicase is bound to the target polynucleotide such that the first helicase controls the movement of the target polynucleotide through the pore; (b) further contacting the target polynucleotide with a second helicase as the first helicase controls the movement of the target polynucleotide through the transmembrane pore, wherein the second helicase binds to an internal polynucleotide of the target polynucleotide at a location on the polynucleotide different than where the first helicase is bound without concurrent binding to a terminal nucleotide of the target polynucleotide, and wherein the second helicase controls movement of the target polynucleotide through the pore after the first helicase disengages from the target polynucleotide; and (c) measuring one or more characteristics of the target polynucleotide during one or more interactions as the target polynucleotide moves through the transmembrane pore, wherein the one or more interactions are measured along a length of the target polynucleotide that comprises at least 500 nucleotides and exceeds processivity of the first helicase, thereby characterizing the target polynucleotide anticipate and make obvious instant claims 31-33 and 57-64 drawn to a method of controlling the movement of a polynucleotide, comprising: contacting the polynucleotide with a DNA-dependent ATPase (Dda) helicase comprising: (a) at least one substitution of an amino acid that
Applicants request for reconsideration of the above rejections based upon claim amendments presented herein is acknowledged, however, is not found persuasive in overcoming the rejection for the reasons stated above.
Claims 31-33 and 57-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of US 10,221,450. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-12 of US 10,221,450 are drawn to method comprising: (a) providing a complex comprising one or more helicases bound, in an active mode, to a polynucleotide, wherein the polynucleotide comprises one or more spacers that are configured such that movement of the one or more helicases relative to the polynucleotide is stalled: (b) contacting a transmembrane pore, which is present in a membrane, with the complex, wherein the transmembrane pore comprises an opening that permits passage of the polynucleotide, but not the one or more helicases, across the membrane; and (c) applying a potential difference across the membrane such that the polynucleotide moves through the transmembrane pore and such that the one or more helicases pass across the one or more spacers of the polynucleotide anticipate and make obvious instant claims 31-33 and 57-64 drawn to a method of controlling the movement of a polynucleotide, comprising: contacting the polynucleotide with a DNA-dependent ATPase (Dda) helicase comprising: (a) at least one substitution of an amino acid that from: motif Ia, motif Ic, motif III, motif IV, motif V, and motif Vb; and/or at any one of positions 88, 89, 98, 121, 150, 152, 276, and 287 wherein the positions are numbered by alignment of the amino acid sequence of the Dda helicase to the amino acid sequence set forth in SEQ ID NO: 8; and (ii) wherein the amino acid that interacts with one or more nucleotides in a single stranded polynucleotide is substituted with: an amino acid in a larger R group, and/or an amino acid that improves interaction of the Dda helicase with the phosphate backbone of the single stranded polynucleotide; and (b)
Applicants request for reconsideration of the above rejections based upon claim amendments presented herein is acknowledged, however, is not found persuasive in overcoming the rejection for the reasons stated above.
The office has made a reasonable attempt at identifying all issued patents and applications subject to a double patenting rejection. Applicants are asked to identify any additional issued patents or applications that the office should be aware of for consideration of double patenting.
Remarks
No claim is allowed.
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1/6/2026
/RICHARD G HUTSON/Primary Examiner, Art Unit 1652