Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 09/29/2022 was filed after the mailing date of the FAOM. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The disclosure is objected to because of the following informalities: paragraph 48 discusses a peptide fragment without an accompanying SEQ ID NO. Pursuant to MPEP 2422 and 37 CFR 1.821(a), any amino acid sequence with at least 4 defined amino acids in length requires a sequence identifier. Additionally, please include a Sequence Listing. Appropriate correction is required.
Drawings
The drawings are objected to because of the following informalities: Figs. 5-6 shows peptide fragments with than four amino acids without accompanying SEQ ID NO. Pursuant to MPEP 2422 and 37 CFR 1.821(a), any amino acid sequence with at least four defined amino acids in length requires a sequence identifier. Additionally, please include a Sequence Listing. Appropriate correction is required.
Claim Objections
Claims 9, 13, and 15 are objected to because of the following informalities:
Claim 9 – “6 types of orthogonal identification nanopores” and should be amended to “six orthogonal identification nanopores”
Claim 13 – “4 types of polypeptides with chargeabilities” and should be amended to “four types of polypeptides with chargeabilities”
Claim 15 – “6 types of orthogonal identification nanopores” should be amended to “six types of orthogonal identification nanopores”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Claims 5-10, and 13-15 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 5-7, 10, and 14-15 recites mutations, but there is no reference sequence or protein with known sequence described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 8 recites “measuring an ion current passing through the pore as the protein or polypeptide moves relative to the pore” and is unclear how it is would be possible to measure “an ion current passing through the pore”, because there is no technique described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 9 recites “using a denaturant and designing and constructing a "tertiary structure unfolding nanopore"”, but there is no technique or tertiary structure unfolding nanopore described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 9 recites “designing functionalized Aerolysin nanopores capable of driving polypeptides with different chargeabilities” and “constructing 6 types of orthogonal identification nanopores”, but there is no technique described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 9 recites “further identifying ion migration frequency characteristics by adopting an ion flow confined perturbation technique”, but there is no technique described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 13 recite “wherein the designing functionalized Aerolysin nanopores capable of driving polypeptides with different chargeabilities”, but there is no technique described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 15 recites “the potential gradient of a current sensing region in the pore is regulated”, but there is no technique described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as failing to set forth the subject matter which the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the applicant regards as the invention.
Claims 1-15 are generally narrative and indefinite, failing to conform with current U.S. practice. They appear to be a literal translation into English from a foreign document and are replete with grammatical and idiomatic errors.
Claim 1 recites the limitation "the polypeptides". There is insufficient antecedent basis for this limitation in the claim. Furthermore, it is unclear how “the polypeptides” are related to “a protein/polypeptide”.
Claim 1 recites the limitation “protein charge screening” and is indefinite because the limitation does not positively recite an action and appears to be a name of a sequencing technique. Furthermore, it is unclear what the “protein charge screening” means because there is no accepted definition in the protein arts.
Claim 1 recites the limitation “orthogonal identification of amino acids” is indefinite because the limitation does not positively recite an action and appears to be a name of a sequencing technique. Furthermore, it is unclear what the “orthogonal identification of amino acids” means because there is no accepted definition in the protein arts.
Claim 1 recites the limitation “confined perturbation-assisted identification of amino acids” is indefinite because the limitation does not positively recite an action and appears to be a name of a sequencing technique. Furthermore, it is unclear what the “confined perturbation-assisted identification of amino acids” means because there is no accepted definition in the protein arts.
Claim 1 recites the limitation “single-molecule protein sequencing” is indefinite because the limitation does not positively recite an action and appears to be a name of a sequencing technique.
Claim 2 recites the limitation “the single protein will be unfolded by a temperature and pH regulation method” is indefinite because the limitation does not positively recite an action performed in the method.
Claim 3 recites the limitation “to obtain an label signal of ion flow starting point” is indefinite because it is unclear how the terminus labeling is related to an ion flow starting point.
Claim 4 recites the limitation “protein charge screening nanopores are designed” is indefinite because the limitation does not positively recite an action. Furthermore, it is unclear what the “protein charge screening” means because there is no accepted definition in the protein arts.
Claim 5 recites “the unfolding of a tertiary structure of the polypeptide of step (4)”. There is insufficient antecedent basis for this limitation in the claim.
Claim 5 recites “open a molecular structure of the polypeptide, i.e., mutant T284/F/Y/IL/W or G214/F/Y/I/L/W” is indefinite because it is unclear whether the narrower range “i.e., mutant T284/F/Y/IL/W or G214/F/Y/I/L/W” is a limitation.
Claim 6 recites “the following six types of orthogonal nanopores”. There is insufficient antecedent basis for this limitation in the claim.
Claim 6 recites “i.e., mutant T218K/R/H/D/E, S278K/R/H/D/E, S276K/R/H/D/E, T274K/R/H/D/E or A224Q/N/D/E/R/K/H”, “i.e., mutant T218N/Q, Q212R/K/H, D209S/T, S276Q/N, D222G/A/S or A224E/D”, “i.e., mutant R220S/T/A, D222G/A, S2361/L/V, G2701/L, T232I/L/V, T274G/A/IL or K23 8F/Y/W”, “i.e., mutant D222W/H/F/Y, S276F/Y, A224K/R/W, S272W/H or T274W/H/F/Y”, “i.e., mutant S276F/Y/I/L, S278F/Y/l/L/P, T274W/P, S236W or K238G/W/I/L/F/Y/P”, “i.e., mutant T218G/A, S276G/A, S278G/A, T274G/A, N226D/E or Q268S/T/G/A” is indefinite because it is unclear whether the narrower ranges of the examples is are limitations.
Claim 7 recites “a perturbation amplification nanopore for the perturbation systems is designed to further improve sequencing accuracy in combination with a specific nanopore” and is unclear whether “improve sequencing accuracy in combination with a specific nanopore” is a positively recites step in the method.
Claim 9 recites “a specific ion flow blocked signal or fluorescent signal is generated at the beginning or the end of the polypeptide” and is unclear how the attached “PNA, an oligonucleotide, a polypeptide chain or an organic functional group” would generate a blocked signal or fluorescent signal.
Claim 9 recites “bionically constructing a central amino acid environment of a proteasome 19S domain at the inlet of the Aerolysin nanopore” and is indefinite because there is no commonly used definition for “bionically constructing”.
Claim 10 recites “FAM, VIC, CY5, HEX or ROX” and is indefinite because these are not IUPAC names or other recognized names of organic functional groups. Furthermore, the specification do not disclose the meanings of “FAM, VIC, CY5, HEX or ROX”.
Claim 12 recites “the electric driving forces”. There is insufficient antecedent basis for this limitation in the claim.
Claim 13 recites “adopting 4 "protein charge screening nanopores" for specifically capturing 4 types of polypeptides” and is unclear if there are 4 different nanopores or if the nanopores are capable of capturing 4 different types of polypeptides.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 1 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Maglia (US20160053300A1 published 02/25/2016).
Regarding claim 1, Magila teaches a method for sequencing a protein/polypeptide using Aerolysin nanopores (aerolysin nanopores allowed the analysis of small peptides – paragraph 2), comprising the following steps:
(1) unfolding of the protein (the volume and shape of the unfolded polypeptide chain is different to that of the globular protein – paragraph 75);
(2) terminus labeling of protein sequencing (two native cysteine residues and Phenylalanine 166 are labeled – paragraph 8);
(3) protein charge screening (“protein charge screening” is not a positively recite an action; see 112b);
(4) unfolding of a tertiary structure of the polypeptides (Thermal unfolding of proteins probed at the single molecule level using nanopores – paragraph 119);
(5) orthogonal identification of amino acids (“orthogonal identification of amino acids” is not a positively recite an action; see 112b);
(6) confined perturbation-assisted identification of amino acids (“confined perturbation-assisted identification of amino acids” is not a positively recite an action; see 112b); and
(7) single-molecule protein sequencing (“single-molecule protein sequencing” is not a positively recite an action; see 112b).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TINGCHEN SHI whose telephone number is (571)272-2538. The examiner can normally be reached M-F 9am-6pm.
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/T.C.S./Examiner, Art Unit 1796
/CHARLES CAPOZZI/Supervisory Patent Examiner, Art Unit 1798