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 .
DETAILED ACTION
Responsive to communication entered 10/17/2025.
Priority
This application, Pub No. US 2024/0019442 A1, published 01/18/2024, is a § 371 National Stage of International Patent Application No. PCT/US21/49836, filed 09/10/2021, Pub. No. WO 2022/056244, published 03/17/2022, which claims benefit of US 63/076,735, filed 09/10/2020, and continuation-in-part of Application No. PCT/US21/14142, filed 01/20/2021, Pub. No. WO 2021/150578, published 07/29/2021, which claims benefit of 62/963,298, filed 01/20/2020.
Status of Claims
Claims 1-16 are currently pending. Claims 1-27 have been originally filed. Claims 1, 3, 7, 9 and 13-15 have been amended, and Claims 17-27 have been cancelled, as set forth in Applicant’s Preliminary amendment filed 03/07/2023. Claims 1-16 have been subject to election/restriction requirement mailed 09/08/2025. Claim 15 has been amended, as set forth in Applicant’s amendment filed 10/17/2025. Claims 13-16 are withdrawn from further consideration. Claims 1-12 are examined.
Election/Restriction
Applicant's election, with traverse, of Group I, Claims 1-12, drawn to a method of method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution,
and the following species:
C0-C2 fragment of human cardiac myosin binding protein-C (cMyBP-C) as a myosin binding protein-C (MyBP-C); and
5-((((2-Iodoacetyl)amino)ethyl)amino)Naphthalene-1-Sulfonic Acid (IAEDANS) and N-[4-(dimethylamino)-3,5-dinitrophenyl]maleimide (DDPM) as two fluorescent probes,
in the reply filed on 10/17/2025 is acknowledged.
Applicant identified Claims 1-12 as encompassing the elected species. Because Applicant did not distinctly and specifically point out the supposed errors in the species election requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Applicant’s traversal of the restriction requirement between Groups I and II is on the ground(s) that:
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This is not found persuasive because, for cases filed under 35 U.S.C. 371 and found to be lacking unity, search burden is not a criterion for the restriction.
The requirement is still deemed proper and is therefore made FINAL.
Claims 13-16 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Information Disclosure Statement
The information disclosure statement, submitted by Applicant on 05/10/2023, is in
compliance with the provisions of 37 CFR 1.97 and 37 CFR 1.98. Accordingly, the information disclosure statement is being considered by the Examiner.
Specification
I. In BACKGROUND OF THE INVENTION, the statement “[0005] Cardiac myosin-binding protein C (cMyBP-C) is the most commonly mutated gene associated with hypertrophic cardiomyopathy (HCM), which can also lead to heart failure (HF)” (Emphasis added) is unclear because one of skill in the art would have known that a gene is a segment of DNA that contains the instructions to make a protein, while a protein is the functional product created from that gene's instructions.
II. The use of the terms ATTO™, Alexa Fluor®, HiPrep™ Sephacryl ® S-100, which are a trade name or a mark used in commerce, have been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
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Claim Objections
Claims 5 and 11 are objected to because of the following informalities: use of acronyms. For clarity, it is recommended to introduce an acronym by placing the acronym in parentheses after the first use of the spelled-out term or name, for example, 5-{[2-(2-Iodoacetamido)ethyl]amino}naphthalene-1-sulfonic acid (IAEDANS).
Claims 5 and 11 are objected to because of the following informalities: missing a coma between recitations “ATTO” and “FMAL.”
Claim 9 is objected to because of the following informalities: improper Markush format. Claim 9 recites “wherein the human MyBP-C comprises a cardiac myosin binding protein-C (cMyBP-C), skeletal MyBP-C, and fragments thereof.” Emphasis added. It is noted that the claim is not indefinite because it is clear what Applicant intends to include in a Markush grouping. However, Applicant is reminded that, according to MPEP § 2173.05(h) Alternative Limitations, when materials recited in a claim are so related as to constitute a proper Markush group, they may be recited in the conventional manner, or alternatively. For example, if "wherein R is a material selected from the group consisting of A, B, C and D" is a proper limitation, then "wherein R is A, B, C or D" shall also be
considered proper.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 112 that form the basis for the rejections under this section made in this Office action.
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 1-12 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1-6, as recited in independent Claim 1, are drawn to:
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Claims 7-12, as recited in independent Claim 7, are drawn to:
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A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, Claims 1 and 7 recite the broad recitation ”a fluorescent protein biosensor”, and the claims also recite “a MyBP-C fluorescent protein biosensor” and “a MyBP-C fluorescent protein biosensor”, respectively which is the narrower statement of the range/limitation. Claims 1 and 7 recite the broad recitation ”quantitating the MyBP-C fluorescent protein biosensor structural changes including phosphorylation”, and the claims also recite “A method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution”, which is the narrower statement of the range/limitation. Emphasis added. Claims 1 and 7 are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claims 2-6 and 8-12 are rejected as being dependent upon the rejected claim(s) and fail to cure its indefiniteness.
Claims 2 and 8 recite the limitation "wherein a physiological change/perturbation, phosphorylation, and/or mutation of the MyBP-C affects a change in structure of the protein, affecting/changing FRET efficiency" in lines 1-3. There is insufficient antecedent basis for this limitation in independent Claims 1 and 7, which are drawn to “A method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution”. Emphasis added.
Claims 6 and 12 recite the limitation "wherein the method is for screening physiological conditions or compounds that affect structural changes of the fluorescent protein biosensor" in lines 1-3. There is insufficient antecedent basis for this limitation in independent Claims 1 and 7, which are drawn to “A method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution”. Emphasis added.
Claims 6 and 12 recite the limitation "wherein the method is for screening physiological conditions or compounds that affect structural changes of the fluorescent protein biosensor" in lines 1-3. There is insufficient antecedent basis for this limitation in independent Claims 1 and 7, which are drawn to “A method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution”. Emphasis added.
Claims 5 and 11 contain the trademark/trade name ATTO™ and Alexa Fluor®. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe dyes and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102 of this title, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-12 are rejected under 35 U.S.C. 103 as obvious over Colson et al., "Site-directed spectroscopy of cardiac myosin-binding protein C reveals effects of phosphorylation on protein structural dynamics," Proc. Natl. Acad. Sci., 2016, vol. 113, No 12, pp. 3233-3238 (IDS submitted on 05/10/2023), Supporting Information attached to the instant Office Action; in view of Levinson et al., US 2019/0361014 A1, published 11/28/2019.
Colson et al., throughout the publication, teach the use of time-resolved fluorescence resonance energy transfer (TR-FRET) to characterize the structural dynamics of the flexible and disordered regions of the cardiac myosin-binding protein C (cMyBP-C) N-terminal fragment C0C2 and assay the structural changes associated with phosphorylation by Protein Kinase A (PKA):
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Emphasis added.
Colson et al. do not specifically teach measuring FRET efficiency when structural changes in the MyBP-C fluorescent protein biosensor occur, wherein FRET efficiency is a proportion of donor molecules that have transferred excitation state energy to acceptor molecules; and c. quantitating MyBP-C fluorescent protein biosensor structural changes including phosphorylation using the measured FRET efficiency.
Levinson et al., throughout the publication, teach a method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution (paragraph [0005]: “methods of making and using the kinase that can be used to directly monitor allosteric structural changes in any kinase domain, from any kinase, upon ligand binding, based on intramolecular distance measurements made by Forster resonance energy transfer (FRET)”; paragraph [0033]: “a direct structural readout of conformational changes in real time in solution”; paragraph [0147]: “the biosensor for TR-FRET measurements”; paragraph [0148]: “incorporating selective labeling sites for TR-FRET, it was desired that the phosphorylation state of AurA also be controllable. The addition of a C290A mutation which favors autophosphorylation at the T288 site, or the addition of a C290S mutation which inhibits autophosphorylation allows for a simple method of isolating phosphorylation states of AurA”), the method comprising:
a. labeling a protein with two fluorescent probes to generate a fluorescent protein biosensor suitable for TR-FRET (paragraph [0148]: “the FRET donor, Alexa 488 maleimide, was conjugated to a cysteine labeling site via the maleimide reaction, … Prior to the addition of the FRET acceptor, Alexa 568 maleimide, to the remaining cysteine labeling site, donor-only labeled sample was set aside to serve as a matched donor-only control in TR-FRET experiments. Final donor-only and donor+acceptor samples +/−phosphorylation and +/−TPX2 peptide were diluted and applied to 384-well assay plates to be read in the fluorescence lifetime plate reader”; paragraph [0059]: “Measuring FRET can additionally or alternatively include acquiring a time-resolved (TR) FRET measurement, which detects the donor fluorophore time-dependent emission waveform after a single excitation pulse. TR-FRET can be measured using direct waveform recording”);
b. measuring FRET efficiency when structural changes in the fluorescent protein biosensor occur, wherein FRET efficiency is a proportion of donor molecules that have transferred excitation state energy to acceptor molecules (“[0095] providing a protein kinase comprising a donor molecule and an acceptor molecule, wherein the protein kinase can exist in at least a first conformation and a second conformation; [0096] wherein in the first conformation, energy is transferred from the donor molecule to the acceptor molecule; [0097] wherein in the second conformation, the efficiency with which energy is transferred from the donor molecule to the acceptor molecule differs from the efficiency with which energy is transferred from the donor molecule to the acceptor molecule in the first conformation; and measuring the proportion of protein kinase in the first conformation”); and
c. quantitating protein structural changes including phosphorylation using the measured FRET efficiency (paragraph [0005]: “the methods include measuring the conformation of a kinase including, for example, the position of the kinase activation loop, an important allosteric structural element modulated by intrinsic regulatory mechanisms and by certain kinase inhibitors. Measurement of the proportion of a kinase in a particular conformation can allow discrimination of the effects of different subtypes of allosteric inhibitors and can provide direct information on the nature of the induced structural change”; paragraph [0031]: “(Förster resonance energy transfer (FRET) can be used to make nanometer-scale distance measurements of the conformational rearrangement. During FRET, an excited fluorophore (the donor, “D”) transfers energy non-radiatively to an acceptor fluorophore (“A”). The efficiency of this transfer, E, is determined by the equation E=1/(1+r/R0)6, where r is the distance between the fluorophores and R0 is the Förster distance for the D and A pair (approximately 1 nanometer (nm)−10 nm), determined by the quantum yield of D and the fluorophores' spectral overlap). FRET is thus highly sensitive to nanometer-scale changes in the distance between D and A).
It would have been prima facie obvious, before the effective filing date of the claimed invention, for one of ordinary skill in the art to have made and used measuring FRET efficiency, taught by Levinson et al., in the TR-FRET method, taught by Colson et al.
One of ordinary skill in the art would have been motivated to have made and used measuring FRET efficiency, taught by Levinson et al., in the TR-FRET method, taught by Colson et al., because it would be desirable to make nanometer-scale distance measurements of the conformational rearrangement using the efficiency of energy transfer from an excited fluorophore (the donor, “D”) to an acceptor fluorophore (“A”), as taught by Levinson et al.
One of ordinary skill in the art would have had a reasonable expectation of success in making and using measuring FRET efficiency, taught by Levinson et al., in the TR-FRET method, taught by Colson et al., because this technique was known in the art of TR-FRET assays for quantification of phosphorylation-mediated structural changes in solution, as taught by Levinson et al.
Regarding Claims 6 and 12, recitation "wherein the method is for screening physiological conditions or compounds that affect structural changes of the fluorescent protein biosensor" is considered as “intended use” because this recitation does not require performing an active process step and, accordingly, carries no patentable weight. The Examiner further notes that, as indicated above, in paragraph [0005], Levinson et al. teach “Measurement of the proportion of a kinase in a particular conformation can allow discrimination of the effects of different subtypes of allosteric inhibitors and can provide direct information on the nature of the induced structural change.”
As such, Colson et al. in combination with Levinson et al. teaches all steps of the instantly claimed method and the elected species (1) C0-C2 fragment of human cardiac myosin binding protein-C (cMyBP-C) (Note: Colson et al. teach “cMyBP-C is likely to be highly phosphorylated under resting physiological conditions in healthy humans and studied mouse models of human heart disease”); and the elected species (2) 5-((((2-Iodoacetyl)amino)ethyl)amino)Naphthalene-1-Sulfonic Acid (IAEDANS).
Neither Colson et al. nor Levinson et al. teach N-[4-(dimethylamino)-3,5-dinitrophenyl]maleimide (DDPM) as a fluorescent probe, which is the elected species (2).
However, as evidenced by Steward et al., US 2003/0143650 A1, published 07/31/2003 (See, for example, Table 6), the use of IAEDANS and DDPM as two fluorescent probes in FRET assays is well-known in the prior art.
Accordingly, it would have been prima facie obvious, before the effective filing date of the claimed invention, for one of ordinary skill in the art to have made and used IAEDANS and DDPM, taught by Steward et al., as two fluorescent probes in the method, taught by combination of Colson et al. and Levinson et al.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GALINA M YAKOVLEVA whose telephone number is (571)270-3282. The examiner can normally be reached on M-F 8:30 AM-5:00 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, GREGORY S EMCH can be reached on (571)272-8149. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/GALINA M. YAKOVLEVA/Primary Examiner, Art Unit 1678