DETAILED ACTION
Note: the current examiner is different from the examiner of the Non-Final Office Action
(1/8/2026).
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 .
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.
Withdrawn Objections/Rejections
The objection to paragraph 5 of the specification is withdrawn in response to the amendments.
The claim objections are withdrawn in response to the amendments.
The 112b rejection of claims 1-4, 6-10 and 12 are withdrawn in response to the amendments.
The 103 rejection of claims 1-6 is withdrawn in response to the amendments. However, new grounds of rejection are set forth below under 102.
Priority
Acknowledgment is made of the present application as a proper National Stage (371) entry of PCT Application No. PCT/US21/49836, filed 09/10/2021, which claims benefit under 35 U.S.C. 119(e) to provisional application No. 63/076,735, filed 09/10/2020. Acknowledgment is also made of the present application as a CIP of PCT Application No. PCT/ US21/14142, filed 01/20/2021, which claims benefit under 35 U.S.C. 119(e) to provisional application No. 62/963,298, filed 01/20/2020.
In consideration of the claim amendments, a new issue of priority is raised.
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application Nos. 63/076,735, 62/963,298 and PCT/ US21/14142 fail to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. Specifically, the limitation “wherein the cMyBP-C fluorescent protein biosensor comprises a first cysteine residue located at Cys 225 in a C1-domain of the cMyBP-C fluorescent protein biosensor and a second cysteine residue located at Cys 330 in an M-domain of the cMyBP-C fluorescent protein biosensor” recited in claim 1 lines 13-16 is not disclosed in the provisional applications or in the PCT/ US21/14142 application and therefore receive no priority benefit.
Claims 7-12 have an effective filing date of 1/20/2020, which is the filing date of Provisional Application No. 62/963,298. Claims 1-6 have an effective filing date of 09/10/2021, which is the filing date of PCT/US21/49836.
Information Disclosure Statement
The information disclosure statement filed 2/25/2026 is being considered by the examiner.
Maintained Specification Objection
Specification
The use of the terms Alexa Fluor® (paras. 44 and 53) and HiPrep™ Sephacryl ® S-100 (para. 66), which are trade names or a marks 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.
Maintained Rejections
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 5 and 11 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 5 and 11 contain the trademark/trade name 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. A person having ordinary skill in the art would question the metes and bounds of the claim.
New Rejections
Claim Rejections - 35 USC § 102
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.
Claims 1-6 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wang, Christopher. (May 2020). SITE-DIRECTED SPECTROSCOPIC LABELING OF CARDIAC MYOSIN-BINDING PROTEIN C FOR INVESTIGATING PROTEIN STRUCTURAL DYNAMICS (Bachelor's thesis, University of Arizona, Tucson, USA).
Regarding claim 1, Wang teaches a method of using time-resolved fluorescence energy transfer (TR-FRET) and a cMyBP-C fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution (“site-directed spectroscopic labeling of cardiac myosin-binding protein c for investigating protein structural dynamics” Title, “FRET probe pairs in cMyBP-C reveal phosphorylation-dependent changes in N-terminal protein structure and dynamics that are important for its regulation of cardiac muscle” Abstract), the method comprising: a. labeling a cardiac myosin-binding protein C (cMyBP-C) with two fluorescent probes to generate a cMyBP-C fluorescent protein biosensor suitable for TR-FRET (“my project aims to lay the foundation for studying cMyBP-C structure through the use of FRET spectroscopy, a technique that allows the measurement of intramolecular distances at the nanometer scale and structural disorder using fluorescent probe pairs. These probes are introduced at cysteine residues within cMyBP-C using thiol-reactive fluorescent dyes” Abstract, “Therefore, to study C0C2 structure and interactions, we will utilize site-specific fluorescent labeling for Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) measurements of N-terminal cMyBP-C structure and dynamics (Colson et al., 2016)” page 9); b. measuring FRET efficiency when structural changes in the cMyBP-C fluorescent protein biosensor occur, wherein FRET efficiency is a proportion of donor molecules that have transferred excitation state energy to acceptor molecules (“Fluorescence lifetimes are used to calculate FRET efficiency and ultimately, the molecular distances and level of molecular order between probe sites” page 10, “Using average lifetimes, FRET efficiencies (proportion of donor molecules that have transferred excitation state energy to acceptor molecules), and % change of FRET efficiency with PKA treatment were calculated” page 21); and c. quantitating cMyBP-C fluorescent protein biosensor structural changes using the measured FRET efficiency (“These values were calculated by Equation 1. and Equation 2. respectively. Equation 3. demonstrates the relationship that FRET efficiency has with distance between donor and acceptor probes. From Equation 3. we can discern that the two have an inverse relationship: as distance between probe sites increases, FRET efficiency decreases” page 21), wherein the cMyBP-C fluorescent protein biosensor comprises a first cysteine residue located at Cys 225 in a C1-domain of the cMyBP-C fluorescent protein biosensor and a second cysteine residue located at Cys 330 in an M-domain of the cMyBP-C fluorescent protein biosensor (“We are able to study human C0C2 with constructs that include FRET probes that are able to be labeled with low non-specific labeling. In this project, H225C,P330C represents such a construct that is able to be used as a FRET biosensor” bridge paragraph pages 41-42, “Space filling model of C1-C2 highlighting the H225C position in C1 and the P330C position in C2)” Figure 1 page 8, see Figure 1 showing Cys 225 and Cys 330).
Regarding claim 2, Wang further teaches wherein phosphorylation-mediated structural changes of the cMyBP-C fluorescent protein biosensor affect FRET efficiency, wherein FRET efficiency is the proportion of the donor molecules that have transferred excitation state energy to the acceptor molecules (“Using average lifetimes, FRET efficiencies (proportion of donor molecules that have transferred excitation state energy to acceptor molecules), and % change of FRET efficiency with PKA treatment were calculated” page 21, “Figure 7. Lifetime data for H225C,P330C DA -PKA and +PKA treatment at pH 6.5 from large-scale experiment shown in Table 2. Lifetimes are plotted in addition to 3 standard deviation bounds for both -PKA (dotted lines) and +PKA (solid lines) separately” page 34).
Regarding claims 3-4, Wang further teaches wherein the cMyBP-C comprises one or more fragments thereof, wherein the one or more fragment of the cMyBP-C comprises a C0-C2 fragment (“hC0C2_H225C,P330C_3nHT (H225C,P330C)” page 13 para. 5 emphasis added).
Regarding claim 5, Wang further teaches wherein the fluorescent probe is selected from the group consisting of 5-((((2-Iodoacetyl)amino )ethyl)amino )Naphthalene-1-Sulfonic Acid (IAEDANS) and fluorescein-5-maleimide (FMAL) (“In labeling and intramolecular TR-FRET experiments with human C0C2, we primarily chose fluorescent dyes such as 5-((((2-Iodoacetyl)amino)ethyl)amino)Naphthalene-1-Sulfonic Acid (IAEDANS) and Fluorescein-5-Maleimide (FMAL) as donor labels and N-(4-Dimethylamino-3,5-Dinitrophenyl)Maleimide (DDPM) as an acceptor label” page 11 para. 2).
Regarding claim 6, Wang further teaches wherein the method is for screening physiological conditions or compounds that affect phosphorylation-mediated structural changes of the cMyBP-C fluorescent protein biosensor (“High-throughput screening FRET experiments on C0C2 may be conducted with tens of thousands of drug compounds to screen for compounds that are able to mimic phosphorylation of C0C2” page 44 para. 2). Note that the claim is considered as reciting “intended use” because this recitation does not require performing an active process step and, accordingly, carries no patentable weight.
Maintained Rejections
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, 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.
Claim(s) 7-12 is/are rejected under 35 U.S.C. 103 as being unpatentable 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 cited on PTO 892 1/8/2026; in view of Levinson et al., US 2019/0361014 A1, published 11/28/2019-cited on PTO 892 1/8/2026.
Regarding claims 7-8, Colson teaches a method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent MyBP-C protein biosensor to quantitate phosphorylation-mediated structural changes in solution (“Site-directed spectroscopy of cardiac myosin-binding protein C reveals effects of phosphorylation on protein structural dynamics” Title, “We have used the site-directed spectroscopies of time-resolved fluorescence resonance energy transfer (TR-FRET)… to resolve the structure and dynamics of cardiac myosin-binding protein C (cMyBP-C), focusing on the N-terminal region… Phosphorylation by PKA in the MyBP-C motif regulates these binding interactions. Our spectroscopic assays detect distances between pairs of site-directed probes on cMyBP-C. We engineered intramolecular pairs of labeling sites within cMyBP-C to measure, with high resolution, the distance and disorder in the protein’s flexible regions using TR-FRET and DEER. Phosphorylation reduced the level of molecular disorder and the distribution of C0C2 intramolecular distances became more compact, with probes flanking either the motif between C1 and C2 or the Pro/Ala-rich linker (PAL) between C0 and C1” Abstract), the method comprising: a. labeling a human myosin-binding protein C (MyBP-C) with two fluorescent probes to generate a MyBP-C fluorescent protein biosensor suitable for TR-FRET (“cMyBP-C site-directed mutagenesis, labeling and phosphorylation. We determined that the C0C2 fragment of cMyBP-C (WT C0-C2) contains a single Cys (C248) that is readily labeled by maleimide-group fluorescent dyes and spin labels, whereas the other 4 Cys in C0C2 are not readily labeled under our labeling conditions. Therefore, we introduced a second reactive Cys to replace a surface accessible Ser residue either in the C0, C1, or C2 domain (S18C, S169C, or S440C) in the three varieties of double-Cys mutants used in this study” Supporting Information page 1 para. 1).
Colson fails to teach b. measuring FRET efficiency when structural changes in the MyBP-C fluorescent protein biosensor occur, wherein FRET efficiency is the proportion of the donor molecules that have transferred excitation state energy to the acceptor molecules and c. quantitating MyBP-C fluorescent protein biosensor structural changes including phosphorylation using the measured FRET efficiency, wherein phosphorylation-mediated structural changes of the MyBP-C fluorescent protein biosensor affect FRET efficiency, wherein FRET efficiency is the proportion of the donor molecules that have transferred excitation state energy to the acceptor molecules.
Levinson teaches a method of using time-resolved fluorescence energy transfer (TR-FRET) and a fluorescent protein biosensor to quantitate phosphorylation-mediated structural changes in solution (“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)” para. 5, “a direct structural readout of conformational changes in real time in solution” para. 33, “the biosensor for TR-FRET measurements” para. 147, “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” para. 147), the method comprising: a. labeling a protein with two fluorescent probes to generate a fluorescent protein biosensor suitable for TR-FRET (“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” para. 148, “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” para. 59); 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 (“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” para. 95; “wherein in the first conformation, energy is transferred from the donor molecule to the acceptor molecule” para. 96; “ 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” para. 97); and c. quantitating protein structural changes including phosphorylation using the measured FRET efficiency (“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” para. 5, “(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” para. 31). Levinson further suggests that steps b-c enable the nanometer-scale distance measurements of the conformational rearrangement of clinically relevant kinases (“this disclosure describes an assay for determining the conformational rearrangement of a kinase. In some embodiments, the conformational rearrangement is of the activation loop of the kinase. In some embodiments, the kinase is a clinically relevant kinase including for example, the kinase Aurora A (AurA), a key regulator of mitosis that has been identified as an oncogene and that has generated interest as a chemotherapeutic drug target” para. 31).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Colson to include steps b-c, wherein phosphorylation-mediated structural changes of the MyBP-C fluorescent protein biosensor affect FRET efficiency, wherein FRET efficiency is the proportion of the donor molecules that have transferred excitation state energy to the acceptor molecules taught by Levinson because Levinson teaches that this enables nanometer-scale distance measurements of the conformational rearrangement of clinically relevant kinases and Colson is interested in the quantification of phosphorylated-mediated structural changes. A person having ordinary skill in the art would have had a reasonable expectation of success because TR-FRET is a known technique in the art of TR-FRET assays for quantification of phosphorylation-mediated structural changes in solution, as taught by Levinson et al. (paras. 31-32 and 59).
Regarding claim 9, Colson in view of Levinson teach the method of claim 7 as discussed above.
Colson in view of Levinson further teach wherein the human MyBP-C comprises a cardiac myosin binding protein-C (cMyBP-C), skeletal MyBP-C, or fragments thereof (“cardiac myosin-binding protein C” Title of Colson).
Regarding claim 10, Colson in view of Levinson teach the method of claim 9 as discussed above.
Colson in view of Levinson further teach wherein the fragment of the MyBP-C comprises the C0-C2 fragment of the MyBP-C (“Phosphorylation reduced the level of molecular disorder and the distribution of C0C2 intramolecular distances became more compact, with probes flanking either the motif between C1 and C2 or the Pro/Ala-rich linker (PAL) between C0 and C1” Abstract of Colson, “we introduced a second reactive Cys to replace a surface accessible Ser residue either in the C0, C1, or C2 domain (S18C, S169C, or S440C) in the three varieties of double-Cys mutants used in this study” Supporting Information page 1 para. 1 of Colson).
Regarding claim 11, Colson in view of Levinson teach the method of claim 7 as discussed above.
Colson in view of Levinson further teach wherein the fluorescent probe is selected from the group consisting of 5-((((2-Iodoacetyl)amino )ethyl)amino )Naphthalene-1-Sulfonic Acid (IAEDANS) and fluorescein-5-maleimide (FMAL) (“For FRET experiments, the extent of labeling was confirmed by UV spectrophotometry, colorimetric protein assay, and mass spectrometry. These values were used to constrain the fits of TR-FRET analysis. The molar ratio of IAEDANS labeling (donor) [1,5-IAEDANS, 5-((((2-Iodoacetyl)amino)ethyl)amino)Naphthalene-1-Sulfonic Acid] (Molecular Probes) per Cys labeling site in double-Cys C0C2 was determined to be 9-22% and 72-89%
for FMal labeling (acceptor) [Fluorescein-5-maleimide] (Molecular Probes) per Cys labeling site” Supporting Information page 1 para. 1 of Colson).
Regarding claim 12, Colson in view of Levinson teach the method of claim 7 as discussed above.
Colson in view of Levinson further teach wherein the method is for screening physiological conditions or compounds that affect phosphorylation-mediated structural changes of the MyBP-C fluorescent protein biosensor (“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” para. 5 of Levinson, “high-throughput screens to discover new kinase inhibitor drug candidates” para. 32 of Levinson). Note that the claim is considered as reciting “intended use” because this recitation does not require performing an active process step and, accordingly, carries no patentable weight.
Response to Arguments
Applicant's arguments filed 3/23/2026 have been fully considered but they are not persuasive.
Regarding the objection to the specification,
Applicant remarks that “the proprietary nature of the marks so used is indicated by "capitalizing each letter of the mark ... ," and Applicant respectfully asserts that the use of said trademarks and/or trade names is therefore in compliance with MPEP 608.0l(v) for this reason as well” (page 9 para. 1).
However, contrary to Applicant’s remark, the specification as currently amended fails to capitalize or include the proper symbol on the trade names Alexa Fluor® (paras. 44 and 53) and HiPrep™ Sephacryl ® S-100 (para. 66). Therefore, the objection is maintained.
Regarding the 112b rejections,
Applicant argues that “Claims 1-6, as well as now-withdrawn claims 7-9 and 11-12 have been amended to clarify the invention and render these claims clear and definite” (page 9 para. 4).
However, contrary to Applicant’s remark, claims 5 and 11 continue to recite the trade name or trade mark Alexa Fluor®, which renders the claims indefinite (see rejection above).
Applicant’s arguments with respect to claim(s) 1-7 under 103 have been considered but are moot because the new ground of rejection under 102 does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Regarding the 103 rejections of claims 7-12,
Applicant argues that “Colson does not have the feature of a Cys225.Cys330 biosensor” (page 11 para. 2).
However, claims 7-12 are not limited to Cys225.Cys330. Therefore, Applicant’s arguments are not persuasive.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FERNANDO IVICH whose telephone number is (703)756-5386. The examiner can normally be reached M-F 9:30-6:00 (E.T.).
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/Fernando Ivich/Examiner, Art Unit 1678
/GREGORY S EMCH/Supervisory Patent Examiner, Art Unit 1678
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