DETAILED CORRESPONDENCE
Status of the Application
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 November 3, 2025 has been entered.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1, 2, 9-15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are pending in the application.
Applicant’s amendment to the claims, filed November 3, 2025, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant’s remarks filed November 3, 2025 in response to the final rejection filed June 2, 2025 are acknowledged and have been fully considered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election filed May 23, 2024, applicant elected without traverse the invention of Group I, pending claims 1, 2, 9-15, 17-20, 22-25, 27-29, 35, 36, and 44-49, the species of GroES as the auxiliary protein or peptide, the species of MspA as the transmembrane protein nanopore, the species of the auxiliary protein or peptide is located outside the lumen of the nanopore, and the species of the auxiliary protein or peptide is attached to the nanopore via one or more covalent bonds in the reply filed July 23, 2024.
Claims 9-11 and 14 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected species, there being no allowable generic or linking claim.
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are being examined on the merits only to the extent the claims read on the elected subject matter as set forth above. In the interest of clarity, it is noted that rejections set forth below may be directed to a non-elected species, which have yet to be searched and examined on the merits because the cited prior art was identified during a search and examination of the elected species as set forth above.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on November 3, 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered by the examiner.
Claim Objections
Claim 2 is objected to in the recitation of “(v) is a transmembrane protein nanopore…wherein the transmembrane protein pore” and in the interest of improving claim form and consistency, it is suggested that the term “pore” be replaced with “nanopore” in the noted phrase.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 2, 12, 13, 15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are rejected under 35 U.S.C. 112(b) as being indefinite in the recitation of “wherein when the auxiliary protein or peptide is CsgF, or a homologue, fragment or modified version thereof, the nanopore is a non-CsgG pore, homologue or modified version thereof” and “wherein when the nanopore is a CsgG pore, or a homologue, fragment or modified version thereof, the auxiliary protein or peptide is not a CsgG nanopore, or a homologue, fragment or modified version thereof” in claims 1 and 36 and the recitation of “the auxiliary protein or peptide is not CsgF or a CsgF peptide or homologue, fragment or modified version thereof; or wherein the auxiliary protein or peptide is not a CsgG nanopore, or a homologue, fragment or modified version thereof” in claims 44 and 47 is withdrawn in view of applicant’s amendments to claims 1, 36, 44, and 47 to delete the phrases at issue.
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are newly rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1 (claims 2, 12, 13, 15, 17-20, 22-25, 27-29, 35, 36, and 44-46 dependent therefrom) and 36 (claims 47-49 dependent therefrom) are indefinite in the recitation of “wherein the nanopore is not a CsgG pore” because it is unclear as to the scope of CsgG pore(s) that is/are excluded by the noted limitation. Regarding the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36, the specification discloses: “[t]he term ‘CsgG pore’ defines a pore comprising multiple CsgG monomers. Each CsgG momomer may be a wild-type monomer from E. coli (SEQ ID NO: 3), wild-type homologues of E. coli CsgG,…or a variant of any thereof” (substitute specification filed March 18, 2025 at p. 23, lines 16-19), and defines “variant” to “encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified or wild-type protein in question and having similar biological and functional activity as the unmodified protein from which they are derived” (substitute specification filed on March 18, 2025 at paragraph bridging pp. 22-23). In view of the specification’s disclosed definitions of “CsgG pore” and “variant,” one of skill in the art would recognize that “CsgG pore” in claims 1 and 36 encompasses wild-type CsgG pores as well as all peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified or wild-type protein in question having similar biological and functional activity as the unmodified protein from which they are derived, which appears to encompass all pores. Thus, the claimed isolated pore complex, while requiring a nanopore component, also appears to exclude all nanopores. However, even if claims 1 and 36 do not exclude all nanopores, it is unclear from the claims and the specification as to which nanopore(s) are intended to be excluded by the recitation of “wherein the nanopore is not a CsgG pore.” It is suggested that applicant clarify the scope of claims 1 and 36, particularly with respect to the limitation “wherein the nanopore is not a CsgG pore.”
Claims 44 and 47 are indefinite in the recitation of “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore” because it is unclear as to the scope of CsgFs, CsgF peptides, and CsgG nanopores that are excluded by the noted limitation. Regarding the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore” in claims 44 and 47, the specification discloses: “‘CsgF peptide’ defines a CsgF peptide that has been truncated from its C-terminal end…and/or is modified to include a cleavage site. The CsgF peptide may be a fragment of wild-type E. coli CsgF…, or of a wild-type homologue of E. coli CsgF…or a variant…of any thereof (substitute specification filed March 18, 2025 at p. 24, lines 3-8); “[t]he term ‘CsgG pore’ defines a pore comprising multiple CsgG monomers. Each CsgG momomer may be a wild-type monomer from E. coli (SEQ ID NO: 3), wild-type homologues of E. coli CsgG,…or a variant of any thereof” (substitute specification filed March 18, 2025 at p. 23, lines 16-19); and defines “variant” to “encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified or wild-type protein in question and having similar biological and functional activity as the unmodified protein from which they are derived” (substitute specification filed on March 18, 2025 at paragraph bridging pp. 22-23). In view of the specification’s disclosed definitions of “CsgF peptide,” “CsgG pore” and “variant,” one of skill in the art would recognize that “CsgF,” “CgsF peptide,” and “CsgG nanopore” in claims 44 and 47 encompasses wild-type CsgF proteins and CsgG nanopores as well as all peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified or wild-type protein in question having similar biological and functional activity as the unmodified protein from which they are derived, which appears to encompass all auxiliary proteins. Thus, the claimed isolated pore complex, while requiring an auxiliary protein component, also appears to exclude all auxiliary proteins. However, even if claims 44 and 47 do not exclude all auxiliary proteins, it is unclear from the claims and the specification as to which auxiliary protein(s) are intended to be excluded by the recitation of “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore.” It is suggested that applicant clarify the scope of claims 44 and 47.
Claim Rejections - 35 USC § 102
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Howorka et al. (WO 2016/034591 A2; cited on the IDS filed on November 16, 2021; hereafter “Howorka”).
As amended, claims 1, 2, 12, 15, 17, 20, 22-25, 27, 29, 35, and 44-46 are drawn to an in vitro system for characterising a target polynucleotide, the system comprising a membrane and a pore complex;
wherein the pore complex comprises: (i) a nanopore located in the membrane, and (ii) an auxiliary protein or peptide attached to the nanopore;
wherein the nanopore and the auxiliary protein or peptide together form a continuous channel across the membrane, the channel comprising a first constriction region and a second constriction region;
wherein the first constriction region is formed by a portion of the nanopore, and wherein the second constriction region is formed by at least a portion of the auxiliary protein or peptide;
wherein the nanopore is not a CsgG pore.
As amended, claims 36 and 47-49 are drawn to an isolated pore complex comprising (i) a nanopore, and (ii) an auxiliary protein or peptide attached to the nanopore;
wherein the nanopore and the auxiliary protein or peptide together define a continuous channel, the channel comprising a first constriction region and a second constriction region;
wherein the first constriction region is formed by a portion of the nanopore, and wherein the second constriction region is formed by at least a portion of the auxiliary protein or peptide;
wherein the nanopore is not a CsgG pore.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description). Howorka teaches a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19). While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the modified CsgG pore of Howorka is not excluded by the phrase “wherein the nanopore is not a CsgG pore” and Howorka anticipates the claims when a first modified CsgG of the CsgG tail-to-tail stacked dimer is considered to be the “nanopore” and a second modified CsgG of the CsgG tail-to-tail stacked dimer is considered to be the “auxillary protein or peptide.”
Regarding claim 13, Howorka teaches the CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the modified CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the modified CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the channel comprising modified CsgG pores of Howorka is considered to be encompassed by the claims.
Therefore, Howorka anticipates claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 as written.
RESPONSE TO REMARKS: Applicant argues claims 1 and 36 have been amended to recite that "the nanopore is not a CsgG pore". According to applicant, Howorka fails to anticipate the claims because Howorka does not disclose any pore complex that does not have a CsgG pore.
Applicant’s arguments are not found persuasive. As stated above, it is entirely unclear from the claims and the specification as to the nanopore(s) that are intended to be excluded by the recitation of “wherein the nanopore is not a CsgG pore” in claims 1 and 36 and in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the modified CsgG pore of Howorka is not excluded by the phrase “wherein the nanopore is not a CsgG pore” and Howorka anticipates the claims when a first modified CsgG of the CsgG tail-to-tail stacked dimer is considered to be the “nanopore” and a second modified CsgG of the CsgG tail-to-tail stacked dimer is considered to be the “auxillary protein or peptide.”
For these reasons, it is the examiner’s position that Howorka anticipates claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 as written.
Claims 1, 2, 12, 13, 15, 17, 18, 20, 29, 35, 36, and 44-49 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ho et al. (Sci. Adv. 1:e1500905, 2015, 8 pages; cited on the IDS filed on November 16, 2021; hereafter “Ho”).
Regarding claims 1, 2, 12, 13, 20, 36, and 44-49, Ho teaches incorporating (covalently linking) the ES loops of GroES into an alpha-hemolysin nanopore to produce a transmembrane co-chaperonin, abbreviated as αHL-GroES (p. 1, column 2; p. 2, Figures 1C and 1D). Figure 1D and Figure 4 of Ho show that the αHL of the transmembrane co-chaperonin is inserted into a lipid bilayer (membrane) with the αHL forming a first constriction and the ES loops of GroES being outside of the lumen of the αHL nanopore and forming a second constriction. The recitation of “for characterising a target polynucleotide” in claim 1 is interpreted as a product-by-process limitation and does not otherwise limit the structural and/or functional properties as set forth in the body of the claim. Given a broadest reasonable interpretation, Ho anticipates the claims when the αHL of αHL-GroES is considered to be the “nanopore” and the ES loops of αHL-GroES are considered to be the “auxillary protein or peptide.”
Regarding claim 15, the recitation of “wherein the auxiliary protein is a modified auxiliary protein or peptide comprising at least one amino acid modification compared to a naturally occurring auxiliary protein or peptide” is a product-by-process limitation and given that the amino acid sequence of the “naturally occurring auxillary protein or peptide” is unlimited, the noted limitation does not otherwise limit the structural and/or functional properties of the auxiliary protein or peptide as set forth in the body of claim 1.
Regarding claim 17, Figure 1B of Ho shows that the αHL nanopore of the transmembrane co-chaperonin has a diameter of 3.2 nm.
Regarding claim 18, Figure 1D of Ho shows that the αHL moiety of αHL-GroES is inserted into a lipid bilayer. Lipids of the lipid bilayer are considered to be amphipathic molecules.
Regarding claim 29, the recitation of “wherein the nanopore is a modified transmembrane protein nanopore comprising at least one amino acid modification compared to a naturally occurring transmembrane protein nanopore” is a product-by-process limitation and given that the amino acid sequence of the “naturally occurring transmembrane protein nanopore” is unlimited, the noted limitation does not otherwise limit the structural and/or functional properties of the nanopore as set forth in the body of claim 1.
Regarding claim 35, Ho teaches single-channel recordings to measure current through the transmembrane co-chaperonin (p. 3, column 2, top), the single-channel recordings were performed using bilayers dividing two chambers, each containing 500 ml of buffer, the electrical signals were amplified by using a patch clamp amplifier with the cis compartment connected to ground, amplified signals were digitized, and data analysis was carried out using Clampfit (p. 6, column 2, bottom).
Therefore, Ho anticipates claims 1, 2, 12, 13, 15, 17, 18, 20, 29, 35, 36, and 44-49 as written.
RESPONSE TO REMARKS: Applicant argues the ES loops introduced into the alpha-hemolysin nanopore do not provide a constriction on top of the αHL-GroES and do not represent an auxiliary protein or peptide that provides a second constriction region as required by the claims and as disclosed in the specification and figures.
Applicant’s arguments are not found persuasive. While the nanopore of Ho is not the same as the specification’s disclosed nanopore with a complete GroES protein ring complexed with a nanopore, the claims do not require a complete GroES protein ring complexed with a nanopore and it is improper to import claim limitations from the specification (MPEP 2111.01.II).
According to MPEP 2111.01.IV.A, where an explicit definition is provided by the applicant for a term, that definition will control interpretation of the term as it is used in the claim. The instant specification defines “constriction region” as referring to an aperture defined by a luminal surface of a pore or pore complex, which acts to allow the passage of ions and target molecules but not other non-target molecules through the pore channel or continuous channel formed by the pore and auxiliary protein or peptide” (substitute specification filed on March 18 at p. 28, lines 20-25). This definition does not define “target molecules” and “other non-target molecules” and given a broadest reasonable interpretation, “target molecules” and “other non-target molecules” are unlimited. Ho teaches the αHL-GroES is hemolytically active (p. 3, Fig. 2A) and thus, one of ordinary skill in the art would recognize the ES loops allow passage of ions and “target molecules,” and since the ES loops are spaced by only a few nanometers (p. 2, Fig. 1B and 1D), one of ordinary skill in the art would have recognized the ES loops exclude passage of “other non-target molecules” that are substantially larger than the spacing of the ES loops. As such, contrary to applicant’s position, the ES loops provide a “constriction” in accordance with the definition disclosed in the specification. Moreover, Howorka teaches the αHL pore has one 1.3 nm-wide inner constriction but also has a 2 nm-wide beta barrel featuring additional reading heads (p. 3, lines 18-19), thus suggesting that αHL itself has two separate constrictions, which can be broadly interpreted as a “nanopore” and an “auxiliary protein.”
Applicant argues that in the αHL-GroES of Ho, the ES loops are positioned above the αHL pore and do not form part of the channel that is embedded in the membrane with the αHL pore and thus does not satisfy the limitation that the nanopore and the auxiliary protein or peptide together form a continuous channel across the membrane, the channel comprising a first constriction region and a second constriction region, and wherein the first constriction region is formed by a portion of the nanopore, and wherein the second constriction region is formed by at least a portion of the auxiliary protein or peptide.
Applicant’s argument is not found persuasive. It appears applicant narrowly interprets the claims to require that the second constriction be embedded within the membrane. However, there is no claim limitation requiring that the second constriction be embedded in the membrane.
For these reasons, it is the examiner’s position that Ho anticipates claims 1, 2, 12, 13, 15, 17, 18, 20, 29, 35, 36, and 44-49 as written.
Claim Rejections - 35 USC § 103
The rejection of claim 28 under 35 U.S.C. 103 as being unpatentable over Howorka in view of Ho is withdrawn in view of the instant amendment to claim 28 to delete the alternative of “CsgG,” thus limiting the recited nanopore to being a transmembrane protein nanopore, wherein the transmembrane protein nanopore is a MspA pore or fragments thereof, and wherein the auxiliary protein is GroES or a fragment thereof.
Claim 28 is newly rejected under 35 U.S.C. 103 as being unpatentable over Ho in view of Laszlo et al. (Methods 105:75-89, 2016; cited on the attached Form PTO-892; hereafter “Laszlo”).
Claim 28 is drawn to the in vitro system according to claim 20, wherein the nanopore is a transmembrane protein nanopore and wherein the transmembrane nanopore is a MspA pore, or fragments thereof, and wherein the auxiliary protein is GroES or a fragment thereof.
The relevant teachings of Ho as applied to claims 1, 2, 12, 13, 15, 17, 18, 20, 29, 35, 36, and 44-49 are set forth above and in the interest of brevity are incorporated here. Notably, Ho teaches incorporating (covalently linking) the ES loops of GroES into an αHL nanopore to produce a transmembrane co-chaperonin, abbreviated as αHL-GroES (p. 1, column 2; p. 2, Figures 1C and 1D) and using the resulting αHL-GroES for attachment of GroEL to study kinetic intermediates by measuring current levels (p. 1, column 2, middle; p. 5, Figure 4 and Figure 4 caption, lines 1-3).
Ho does not teach or suggest incorporating GroES or fragments thereof to a MspA pore.
Laszlo teaches nanopores such as biological pores can be used to infer properties of a molecule based on the alteration in current flowing through the pore (p. 76, column 1, middle). Laszlo teaches αHL, which is the nanopore used in Ho, and MspA as exemplary biological pores (p. 76, column 1, middle). Laszlo teaches the use of nanopores to study single molecule kinetics (p. 80, column 1) including enzyme kinetics (p. 80, columns 1-2).
In view of the combined teachings of Ho and Laszlo, it would have been obvious to one of ordinary skill in the art before the effective filing date to substitute αHL of Ho’s αHL-GroES with MspA. One would have been motivated to do this because Ho teaches αHL-GroES and using αHL-GroES to attach to GroEL and study kinetic intermediates by measuring current levels, Laszlo taught αHL and MspA as exemplary biological pores that can be used to infer properties of a molecule based on the alteration in current flowing through the pore, and Laszlo taught the use of nanopores to study single molecule kinetics including enzyme kinetics. Therefore, the system of claim 28 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim Rejections - 35 USC § 101
The rejection of claims 1, 2, 13, 15, 17, 18, 20, 29, 36, and 44-49 under 35 U.S.C. 101 is withdrawn in view of applicant’s amendment to claims 1 and 36 to recite “wherein the nanopore is not a CsgG pore.” As stated above, it is entirely unclear from the claims and the specification as to the nanopore(s) that are intended to be excluded by the recitation of “wherein the nanopore is not a CsgG pore” in claims 1 and 36 and in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, a naturally-occurring membrane and pore complex of a bacterial cell is excluded by the claims.
Claim Rejections - 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 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.
The rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 10,400,014 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49, and further in view of Ho,
the rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,034,734 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49, and further in view of Ho,
the rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,597,970 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho
the rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,685,949 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho
the rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,018,326 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho,
the rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 3 of U.S. Patent No. 12,227,800 (cited on Form PTO-892 filed June 2, 2025) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho,
the provisional rejection of claim 28 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 48 of co-pending application no. 18/313,079 (reference application) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho,
the provisional rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claim 49 of co-pending application no. 18/665,109 (reference application) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho,
the provisional rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claims 1, 15, and 17 of co-pending application no. 19/013,448 (reference application) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho, and
the provisional rejection of claim 28 on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 2 of co-pending application no. 19/069,041 (reference application) in view of Howorka as applied to claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 above, and further in view of Ho
are withdrawn in view of the instant amendment to claim 28 to delete the alternative of “CsgG,” thus limiting the recited nanopore to being a transmembrane protein nanopore, wherein the transmembrane protein nanopore is a MspA pore or fragments thereof, and wherein the auxiliary protein is GroES or a fragment thereof.
U.S. Patent No. 10,400,014 B2
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 10,400,014 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites an apparatus for characterizing a target analyte, the apparatus comprising a mutant CsgG monomer comprising a variant of the sequence shown in SEQ ID NO: 390, wherein the variant comprises a mutation at one or more of positions Y51, N55 and F56, and an in vitro membrane, wherein the monomer is inserted into the in vitro membrane.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claim of the patent does not recite an auxiliary protein or peptide attached to the CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding instant claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the mutant CsgG monomer of the claim(s) of the patent to be a mutant CsgG stacked dimer as taught by Howorka with a first mutant CsgG of a mutant CsgG stacked dimer as the “nanopore” and a second mutant CsgG of a mutant CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding instant claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding instant claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding instant claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding instant claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding instant claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding instant claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding instant claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding instant claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding instant claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” a mutant CsgG stacked dimer of the combination of the claim of the patent and Howorka is considered to be encompassed by the claims.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the patent in view of Howorka.
U.S. Patent No. 11,034,734 B2
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,034,734 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites an apparatus comprising a transmembrane protein pore inserted into an in vitro membrane, wherein the transmembrane protein pore comprises at least one CsgG monomer having amino acid mutations at two or more positions corresponding to Y51, N55, and F56 of the sequence shown in SEQ ID NO: 390.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claim of the patent does not recite an auxiliary protein or peptide attached to the mutant CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the mutant CsgG monomer of the claim(s) of the patent to be a mutant CsgG stacked dimer as taught by Howorka with a first mutant CsgG of a mutant CsgG stacked dimer as the “nanopore” and a second mutant CsgG of a mutant CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding instant claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” a mutant CsgG stacked dimer of the combination of the claim of the patent and Howorka is considered to be encompassed by the claims.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are unpatentable over the claim(s) of the patent in view of Howorka.
U.S. Patent 11,572,387 B2
Claims 36 and 47-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 8 of U.S. Patent 11,572,387 B2 (cited on the IDS filed on July 23, 2024). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding instant claims 36, 48, and 49, claim 1 of the patent recites a pore comprising a CsgG pore and a modified CsgF peptide, wherein the modified CsgF peptide is bound to CsgG and forms a constriction in the pore, wherein the modified CsgF peptide is a truncated CsgF peptide lacking the C-terminal head domain of CsgF and at least part of the neck domain of CsgF, and wherein the CsgF peptide comprises one or more amino acid substitutions; and
claim 8 recites wherein the CsgG pore comprises at least one monomer comprising one or more modification.
Claim 1 of the patent does not recite the CsgG pore comprises a constriction. However, given that the specification of the patent can be used to “learn the meaning of a term in the claim” (MPEP 804.II.B.1) and the specification of the patent describes the CsgG pore as comprising a constriction (column 21).
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claim 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the modified pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
Regarding claim 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claim 47 of this application.
Therefore, claims 36 and 47-49 of this application are unpatentable over claim 1 of the patent.
Claims 1, 2, 12, 13, 15, 17, 18-20, 22-25, 27, 29, 35, and 44-46 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6, 8 and 9 of U.S. Patent 11,572,387 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites a pore comprising a CsgG pore and a modified CsgF peptide, wherein the modified CsgF peptide is bound to CsgG and forms a constriction in the pore, wherein the modified CsgF peptide is a truncated CsgF peptide lacking the C-terminal head domain of CsgF and at least part of the neck domain of CsgF, and wherein the CsgF peptide comprises one or more amino acid substitutions,
claim 6 of the patent recites (in relevant part) the pore according to claim 1, wherein the CsgF peptide and the CsgG pore are covalently coupled,
claim 8 of the patent recites (in relevant part) the pore according to claim 1, wherein the CsgG pore comprises at least one monomer comprising one or more modification, and
claim 9 of the patent recites the pore according to claim 1, which is a double pore comprising two CsgG pores, wherein the modified CsgF peptide is inserted into the lumen of at least one of the CsgG pores.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claim 1 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite the CsgG pore comprises a constriction. However, given that the specification of the patent can be used to “learn the meaning of a term in the claim” (MPEP 804.II.B.1) and the specification of the patent describes the CsgG pore as comprising a constriction (column 21).
The claims of the patent do not recite a membrane as recited in claim 1 of this application and do not recite the limitations of claims 12, 17-19, 24, 25, 27, 28, and 35 of this application.
Regarding claims 12 and 17, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG double pore is homo-oligomeric and a second CsgG of the CsgG double pore is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claim 44, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claim 44 of this application.
In view of Howorka, it would have been obvious to one of ordinary skill in the art to modify the pore of the claims of the patent according to the teachings of Howorka. One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore.
Therefore, claims 1, 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-46 are unpatentable over claims 1, 6, 8 and 9 of the patent in view of Howorka.
U.S. Patent No. 11,597,970 B2
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,597,970 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites a mutant CsgG monomer comprising a variant of the sequence shown in SEQ ID NO: 2 which comprises R192D, R192F, R192S, or R192T.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claim(s) of the patent do not recite an auxiliary protein or peptide attached to the CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27-29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the patent to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” a mutant CsgG stacked dimer of the combination of the claim of the patent and Howorka is considered to be encompassed by the claims.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the patent in view of Howorka.
U.S. Patent No. 11,685,949 B2
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,685,949 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites a mutant CsgG monomer comprising a variant of the sequence shown in SEQ ID NO: 2 which
(a) comprises:
R97W;
R93W;
R93Y and R97Y; or
F191T; and/or
(b) consisting of deletion of V105, A106 and I107; and/or
(c) comprises deletion of one or more of positions R192, F193, I194, D195, Y196, Q197, R198, L199, L200 and E201.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite an auxiliary protein or peptide attached to the CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the patent to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” a mutant CsgG stacked dimer of the combination of the claim of the patent and Howorka is considered to be encompassed by the claims.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the patent in view of Howorka.
U.S. Patent 11,945,840 B2
Claims 36 and 47-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent 11,945,840 B2 (cited on the IDS filed on July 23, 2024). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding instant claims 36, 48, and 49, claim 1 of the patent recites an isolated pore complex comprising:
(i) a modified CsgG pore, wherein the CsgG constriction loop of the CsgG pore comprises one or more deletions; and
(ii) a modified CsgF peptide, wherein the modified CsgF peptide is bound to and forms a constriction in the modified CsgG pore, and wherein the CsgF peptide is truncated and lacks the C-terminal head domain of CsgF and at least part of the neck domain of CsgF.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claim 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
Regarding claim 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claim 47 of this application.
Therefore, claims 36 and 47-49 of this application are unpatentable over claim 1 of the patent.
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, and 44-46 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, 10, and 11 of U.S. Patent 11,945,840 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites an isolated pore complex comprising:
(i) a modified CsgG pore, wherein the CsgG constriction loop of the CsgG pore comprises one or more deletions; and
(ii) a modified CsgF peptide, wherein the modified CsgF peptide is bound to and forms a constriction in the modified CsgG pore, and wherein the CsgF peptide is truncated and lacks the C-terminal head domain of CsgF and at least part of the neck domain of CsgF,
claim 8 of the patent recites (in relevant part) the pore according to claim 1, wherein the CsgF peptide and the CsgG pore are covalently coupled,
claim 10 of the patent recites (in relevant part) the pore according to claim 1, wherein the CsgG pore comprises at least one monomer comprising one or more modification, and
claim 11 of the patent recites the pore according to claim 1, which is a double pore comprising two CsgG pores, wherein the modified CsgF peptide is inserted into the lumen of at least one of the CsgG pores.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite a membrane as recited in claim 1 of this application and do not recite the limitations of claims 12, 17-19, 24, 25, 27, 35, and 44-46 of this application.
Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art to modify the pore of the claims of the patent according to the teachings of Howorka. One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore.
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG double pore is homo-oligomeric and a second CsgG of the CsgG double pore is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 28, in view of the indefiniteness of the function of the recited “functional homologue” of GroES, a CsgF of a CsgG-CsgG complex is considered to be encompassed by “functional homologue” of GroES in claim 28.
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claim 44, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claim 44 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-46 are unpatentable over claims 1, 8, 10, and 11 of the patent in view of Howorka.
U.S. Patent No. 12,018,326 B2
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,018,326 B2 (cited on the IDS filed on July 23, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites an apparatus comprising a transmembrane protein pore inserted into an in vitro membrane, wherein the transmembrane protein pore comprises at least one CsgG monomer comprising a variant having 80% sequence identity to the amino acid sequence of SEQ ID NO: 2,wherein the variant comprises a substitution at position K94 selected from K94N, K94Q, K94R, K94F, K94Y, K94W, K94L, and K94S, and wherein the transmembrane pore facilitates translocation of an analyte through the transmembrane pore.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the variant CsgG pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claim(s) of the patent do not recite an auxiliary protein or peptide attached to the CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the patent to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” a mutant CsgG stacked dimer of the combination of the claim of the patent and Howorka is considered to be encompassed by the claims.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the patent in view of Howorka.
U.S. Patent 12,084,477 B2
Claims 36 and 47-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent 12,084,477 B2 (cited on Form PTO-892 filed September 19, 2024). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding instant claims 36, 48, and 49, claim 1 of the patent recites a pore comprising a CsgG pore and a CsgF peptide, wherein the CsgF peptide is bound to CsgG and forms a constriction in the pore, wherein the CsgF peptide is a truncated CsgF peptide lacking the C-terminal head domain of CsgF and at least part of the neck domain of CsgF, wherein the CsgF peptide is a homologue of SEQ ID NO: 6, and wherein the CsgF peptide comprises one or more amino acid substitutions relative to SEQ ID NO: 6. Claim 1 of the patent does not recite the CsgG pore comprises a constriction. However, given that the specification of the patent can be used to “learn the meaning of a term in the claim” (MPEP 804.II.B.1) and the specification of the patent describes the CsgG pore as comprising a constriction (column 21).
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claim 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
Regarding claim 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claim 47 of this application.
Therefore, claims 36 and 47-49 of this application are unpatentable over claim 1 of the patent.
Claims 1, 2, 12, 13, 15, 17, 18-20, 22-25, 27, 29, 35, and 44-46 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 6-8 of U.S. Patent 12,084,477 B2 (cited on Form PTO-892 filed September 19, 2024) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites a pore comprising a CsgG pore and a CsgF peptide, wherein the CsgF peptide is bound to CsgG and forms a constriction in the pore, wherein the CsgF peptide is a truncated CsgF peptide lacking the C-terminal head domain of CsgF and at least part of the neck domain of CsgF, wherein the CsgF peptide is a homologue of SEQ ID NO: 6, and wherein the CsgF peptide comprises one or more amino acid substitutions relative to SEQ ID NO: 6,
claim 6 of the patent recites (in relevant part) the pore according to claim 1, wherein the CsgF peptide and the CsgG pore are covalently coupled,
claim 7 of the patent recites (in relevant part) the pore according to claim 1, wherein the CsgG pore comprises at least one monomer comprising one or more modification, and
claim 8 of the patent recites the pore according to claim 1, which is a double pore comprising two CsgG pores, wherein the modified CsgF peptide is inserted into the lumen of at least one of the CsgG pores.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claim 1 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the modified CsgG pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite the CsgG pore comprises a constriction. However, given that the specification of the patent can be used to “learn the meaning of a term in the claim” (MPEP 804.II.B.1) and the specification of the patent describes the CsgG pore as comprising a constriction (column 22).
The claims of the patent do not recite a membrane as recited in claim 1 of this application and do not recite the limitations of claims 12, 17-19, 24, 25, 27, 28, 35, and 44-46 of this application.
Regarding claims 1, 12, and 17, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG double pore is homo-oligomeric and a second CsgG of the CsgG double pore is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
In view of Howorka, it would have been obvious to one of ordinary skill in the art to modify the pore of the claims of the patent according to the teachings of Howorka. One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore.
Regarding claim 44, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claim 44 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-46 are unpatentable over claims 1 and 6-8 of the patent in view of Howorka.
U.S. Patent No. 12,227,800 B2
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 3 of U.S. Patent No. 12,227,800 (cited on Form PTO-892 filed June 2, 2025) in view of Howorka. Although the claim(s) at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the patent recites a hetero-oligomeric pore derived from CsgG comprising at least one mutant monomer comprising a variant of the sequence shown in SEQ ID NO: 2 which comprises R192D, R192Q, R192F, R192S, or R192T substitution, and claim 3 of the patent recites a kit for characterising a target analyte comprising (a) a pore according to claim 17 and (b) the components of a membrane.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the modified CsgG pore of the claim(s) of the patent is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite an auxiliary protein or peptide attached to the CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the patent to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding the limitation “wherein when the nanopore is a CsgG pore, or a homologue, fragment or modified version thereof, the auxiliary protein or peptide is not a CsgG nanopore, or a homologue, fragment or modified version thereof” in instant claims 1 and 36, as stated above, given a broadest reasonable interpretation, the phrase “wherein when the nanopore is a CsgG pore, or a homologue, fragment or modified version thereof, the auxiliary protein or peptide is not a CsgG nanopore, or a homologue, fragment or modified version thereof” is interpreted as meaning when the nanopore is any protein or peptide having any function, the auxiliary protein or peptide is not any protein or peptide having any function and given the indefiniteness of this limitation, the CsgG of the claim(s) of the patent, being a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide” is considered to be encompassed by the claims of this application.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 28, in view of the indefiniteness of the function of the recited “functional homologue” of GroES, a CsgG of the CsgG tail-to-tail stacked dimer is considered to be encompassed by “functional homologue” of GroES in claim 28.
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claims 44 and 47 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the patent in view of Howorka.
U.S. Patent Application 18/313,079
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 48 of co-pending application no. 18/313,079 (reference application) in view of Howorka. Although the claim(s) at issue are not identical, they are not patentably distinct from each other.
Claim 48 of the reference application recites a hetero-oligomeric pore derived from CsgG comprising at least one mutant monomer, wherein the mutant monomer comprises a variant of the sequence shown in SEQ ID NO: 2 which (a) comprises: R97W; R93W; R93Y and R97Y; or F191T; and/or (b) consisting of deletion of V105, A106 and 1107; and/or (c) comprises deletion of one or more of positions R192, F193, 1194, D195, Y196, Q197, R198, L199, L200 and E201.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim(s) of the reference application is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the reference application do not recite an auxiliary protein or peptide attached to the CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27-29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the reference application to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claims 44 and 47 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the reference application in view of Howorka. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
U.S. Patent Application 18/665,109
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 49 of co-pending application no. 18/665,109 (reference application) in view of Howorka. Although the claim(s) at issue are not identical, they are not patentably distinct from each other.
Claim 49 of the reference application recites a Kit for characterizing a target polynucleotide comprising a transmembrane protein pore that comprises at least one CsgG monomer comprising a variant having 80% sequence identity to the amino acid sequence of SEQ ID NO: 2, wherein the variant comprises a substitution at position K94 selected from K94N, K94Q, K94R, K94F, K94Y, K94W, K94L, and K94S, and wherein the transmembrane pore facilitates translocation of an analyte through the transmembrane pore.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim(s) of the reference application is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the reference application do not recite an auxiliary protein or peptide attached to the CsgG monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27-29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the reference application to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claims 44 and 47 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the reference application in view of Howorka. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
U.S. Patent Application 18/668,987
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 6 of co-pending application no. 18/668,987 (reference application) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 6 of the reference application recites a transmembrane double pore forming a channel through a membrane, comprising a first CsgG pore, or a homologue thereof, whose tail is associated with the tail of a second CsgG pore, or a homologue thereof, wherein:
(i) the first CsgG pore, or homologue thereof, is a homooligomer and the second CsgG pore, or homologue thereof, is a homooligomer, and the first CsgG pore, or homologue thereof, comprises monomers that have a different amino acid sequence from the monomers of which the second CsgG pore, or homologue thereof, is comprised;
(ii) the first CsgG pore, or homologue thereof, is a homooligomer and the second CsgG pore, or homologue thereof, is a homooligomer, and the first CsgG pore, or homologue thereof, and/or the second CsgG pore, or homologue thereof is not a wild-type pore;
(iii) the first CsgG pore, or homologue thereof, is a heterooligomer and the second CsgG pore, or homologue thereof, is a homooligomer;
(iv) the first CsgG pore, or homologue thereof, is a homooligomer and the second CsgG pore, or homologue thereof, is a heterooligomer; or
(v) the first CsgG pore, or homologue thereof, is a heterooligomer and the second CsgG pore, or homologue thereof, is a heterooligomer, and
wherein at least one residue at the interface between the first CsgG pore, or homologue thereof, and the second CsgG pore, or homologue thereof, is bulkier than the residue present at the corresponding position in a wild type CsgG pore monomer.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the CsgG pore of the claim(s) of the reference application is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite first and second constriction regions as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the reference application to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claims 44 and 47 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the reference application in view of Howorka. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
U.S. Patent Application 19/013,448
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 47 of co-pending application no. 19/013,448 (reference application) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 47 of the reference application recites a kit for characterising a target analyte, the kit comprising: (a) a CsgG pore comprising a mutant monomer which is a variant of the amino acid sequence set forth in SEQ ID NO: 2, and the variant comprises R192D, R192Q, R192F, R192S, or R192T substitutions; and (b) the components of a membrane.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim(s) of the reference application is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite an auxiliary protein or peptide attached to the CsgG mutant monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the reference application to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claims 44 and 47 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the reference application in view of Howorka. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
U.S. Patent Application 19/069,041
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 89 of co-pending application no. 19/069,041 (reference application) in view of Howorka. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 89 of the reference application recites a kit comprising: (i) a CsgG pore that comprises at least one CsgG monomer, wherein the CsgG monomer comprises amino acid mutations at two or more of positions corresponding to Y51, N55 and F56 of the amino acid sequence of SEQ ID NO: 390; and (ii) components of a membrane.
While the intended meaning of the phrase “wherein the nanopore is not a CsgG pore” in claims 1 and 36 is entirely unclear for reasons set forth above, in the interest of advancing prosecution, the recitation of “CsgG pore” in the phrase “wherein the nanopore is not a CsgG pore” is interpreted as a wild-type or naturally-occurring CsgG pore and the phrase “wherein the nanopore is not a CsgG pore” is interpreted as excluding a wild-type or naturally-occurring CsgG pore. In view of this interpretation, the mutant CsgG pore of the claim(s) of the reference application is not excluded by the phrase “wherein the nanopore is not a CsgG pore.”
The claims of the patent do not recite an auxiliary protein or peptide attached to the CsgG mutant monomer as recited in claims 1 and 36 of this application and do not recite the limitations of claims 2, 12, 13, 15, 17, 18, 20, 22-25, 27, 29, 35, and 44-49.
Regarding claims 1, 2, 12, 17, 20, 22, 23, 36, 45, 46, 48, and 49, Howorka teaches that the CsgG channel is a trans-membrane oligomeric protein that forms a channel with a minimum diameter of approximately 0.9 nm (paragraph bridging pp. 2-3). Howorka teaches that CsgG comprises a narrow inner constriction in the channel of the CsgG pore (p. 3, first full paragraph). Howorka teaches CsgG pores in the form of a non-native tail-to-tail stacked dimer (paragraph bridging pp. 119-120; Figures 47 and 52). Howorka teaches the CsgG tail-to-tail stacked dimer as a membrane-embedded pore used in single-channel current traces (e.g., p. 13, Figure 52 description).
In view of Howorka, it would have been obvious to one of ordinary skill in the art for the CsgG of the claim(s) of the reference application to be a CsgG stacked dimer as taught by Howorka with a first CsgG of a CsgG stacked dimer as the “nanopore” and a second CsgG of a CsgG tail-to-tail stacked dimer as the “auxillary protein or peptide.” One would have been motivated to and would have had a reasonable expectation of success to do this because the claims of the patent and Howorka are both related to a CsgG pore and Howorka provides direction and guidance regarding a CsgG pore, particularly use of a CsgG stacked dimer as a membrane-embedded pore used in single-channel current traces.
Regarding claim 13, Howorka teaches the wild type E. coli CsgG pore includes two channel constrictions (p. 24, line 4). Given a broadest reasonable interpretation, Howorka anticipates claim 13 when the portion of the CsgG comprising the first constriction is considered to be the “nanopore” and the portion of the CsgG comprising the second constriction is considered to be the “auxillary protein or peptide.”
Regarding claims 15 and 29, Howorka teaches the CsgG biological pore is a modified CsgG pore, wherein the modified CsgG pore has at least one modification to the monomeric wild-type E-coli CsgG polypeptide sequence in at least one of the CsgG monomers forming the CsgG pore (p. 4, lines 4-6), and teaches the modification is, e.g., a substitution of the naturally occurring amino acid (p. 4, lines 18-19).
Regarding claim 18, Howorka teaches single-channel current recordings of the CsgG in a phospholipid bilayer (p. 141, lines 31-33). Howorka teaches the lipids comprise two hydrophobic tail groups (p. 91, line 5) and thus, the lipids of the phospholipid bilayer are considered to be amphipathic molecules.
Regarding claim 19, Howorka teaches the membrane comprises a solid state layer (p. 91, line 38).
Regarding claim 24, Howorka teaches the pore is a homo-oligomer comprising identical monomers (p. 64, lines 6-7).
Regarding claim 25, Howorka teaches the pore is a hetero-oligomeric pore (p. 61, lines 1-3).
Regarding claim 27, when a first CsgG of the CsgG tail-to-tail stacked dimer is homo-oligomeric and a second CsgG of the CsgG tail-to-tail stacked dimer is hetero-oligomeric, the CsgG monomers of the CsgG tail-to-tail stacked dimer are considered to be “different transmembrane protein nanopore types.”
Regarding claim 35, Howorka teaches the single-channel current recordings were performed using a 16-channel multielectrode cavity comprising a potassium chloride solution and transmembrane currents were recorded using a Tecella Triton 16-channel amplifier and current traces were analysed using the Clampfit of the pClamp suite (p. 148, lines 12-24).
Regarding claims 44 and 47, given the indefiniteness of the phrase “wherein the auxiliary protein or peptide is not CsgF or a CsgF peptide; or wherein the auxiliary protein is not a CsgG nanopore,” the pore of the claim(s) of the patent is considered to be encompassed by the pore of claims 44 and 47 of this application.
Therefore, claims 1, 2, 12, 13, 15, 17-20, 22-25, 27, 29, 35, 36, and 44-49 are unpatentable over the claim(s) of the reference application in view of Howorka. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The examiner has made an earnest attempt to identify those patents and co-pending applications for purposes of rejecting or provisionally rejecting the claims for double patenting. In the interest of compact prosecution, the examiner requests that: 1) the applicant identify any patent(s) and/or co-pending application(s) that claim(s) subject matter that may necessitate a new double patenting rejection, an obviousness-type double patenting rejection, a provisional double patenting rejection, or a provisional obviousness-type double patenting rejection; 2) identify the claims of the patents and/or co-pending applications that claim identical or similar subject matter; 3) identify the corresponding claims of the instant application, and 4) in the interest of compact prosecution, take the appropriate action, e.g., cancel claims to preempt a statutory double patenting rejection and/or file a terminal disclaimer to preempt an obvious-type double patenting rejection or provisional rejection. Applicants’ cooperation in following steps 1) to 4) above is appreciated as this will allow the examiner to focus on more substantive issues in the examination of the instant application.
Conclusion
Status of the claims:
Claims 1, 2, 9-15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are pending in the application.
Claims 9-11 and 14 are withdrawn from consideration.
Claims 1, 2, 12, 13, 15, 17-20, 22-25, 27-29, 35, 36, and 44-49 are rejected.
No claim is in condition for allowance.
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/David Steadman/Primary Examiner, Art Unit 1656