DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant's election with traverse of Group I, claims 1-19, in the reply filed on 20 March 2026 is acknowledged. The traversal is on the ground(s) that conduction a prior art search and examining the indicator recited in claims 1-19 necessarily will include considering prior art applicable to claim 20. Applicant alleges that the subject matter of both Groups I-II could be examined simultaneously without a significant burden on the examiner.
These arguments are found persuasive. Accordingly, the restriction requirement between Groups I-II, as laid out in the previously pending Requirement for Restriction/Election filed 9 February 2026, has been withdrawn.
With regard to the species election, Applicant has elected calcium as the analyte species (see claims 14-17), claims 18-19 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim.
For the purposes of examination, the species of mutations present in claims 7-8 have been fully rejoined.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Rejections - 35 USC § 103
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 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.
The factual inquiries 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-3, 13-17, and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Deo (Nature chemical biology 17.6 (1 April 2021): 718-723) in view of Frei (Nature methods 19.1 (16 December 2021): 65-70).
Regarding claim 1, Deo is drawn towards a study concerned with the use of Halotag as a general scaffold for tunable chemigenetic indicators (Abstract). Deo teaches the use of an engineered chemigenetic indicator that can detect the presence of calcium (i.e., an analyte), termed HaloCaMP, comprising (a) a sensor domain (i.e., termed CaM), (b) a self-labeling tag (i.e., termed cpHaloTag) that is fused to the ASD, and (c) a fluorescent dye that is conjugated to a ligand for the cpHaloTag (pg. 719-720; see Figs. 1-2). Deo teaches that the bioavailable dye-ligand JF525 could be utilized by the invention in order to aid in the partitioning of the sensor in and out of membranes, albeit resulting in a smaller fluorescent change when compared to JF635 (pg. 723). Deo teaches that the HaloCaMP can be utilized to detect the presence of calcium via the emission of a fluorescent signal in the presence of the analyte (pg. 719-720; see Figs. 1-2).
Deo does not teach or suggest that the SLP has a tryptophan-modification (Claim 1).
Frei is drawn towards a study concerned with engineered HaloTag variants for fluorescence lifetime multiplexing (Abstract). Frei teaches the generation of HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines (Abstract) Frei teaches the use of a HaloTag variant, termed HaloTag11, that comprises an M175W mutation (i.e., a tryptophan modification) (pg. 65). Frei teaches that the HaloTag11 was able to bind to fluorescent TMR (i.e., a rhodamine dye) and emit a weaker detectable signal when compared to HaloTag7 (pg. 65). Frei teaches that the proximity of TMR to the introduced tryptophan suggests that photoinduced electron transfer (PET) quenching of the fluorophore is responsible for the decreased quantum yields (pg. 65). Frei teaches that HaloTag11 was more photostable when compared to the unmutated HaloTag7 and recommends the use of HaloTag11 in multiplexing of different species of HaloTags (pg. 68).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention modify the SLP of Deo via the introduction of a tryptophan modification because it would have merely amounted to a simple combination of prior art elements according to known methods to yield predictable results. Because Frei teaches the using a mutated HaloTag protein used for a similar purpose as Deo, namely the self-labeling of the HaloTag protein through the use of a rhodamine dye, then one would have had a reasonable expectation of success in mutating the HaloTag protein of Deo via the introduction of a tryptophan modification and maintaining the HaloTag’s ability to self-label with a rhodamine dye. And because Frei teaches that the introduced tryptophan modification resulted in a more photostable tag, one would have been motivated to do so.
Regarding claim 2, Frei teaches that the proximity of TMR to the introduced tryptophan suggests that photoinduced electron transfer (PET) quenching of the fluorophore is responsible for the decreased quantum yields (i.e., Frei teaches that the tryptophan-modification partially quenches, yet allows fluorescence when it interacts with the fluorescent dye) (pg. 65).
Regarding claim 3, it is noted that the term “about” is defined in the instant specification as encompassing variations of ±20% ([0061]).
Frei teaches that the different possible locations of the mutated tryptophan located at position 175 of HaloTag11 are within 5.0-5.9 Å (i.e., about 5 Å) from the fluorescent dye (see Supplementary Figure S5).
Regarding claims 13-15, Deo teaches that the ASD undergoes a confirmational change when bound to calcium that allows for the emission of the fluorescent signal (pg. 720; see Fig. 2).
Regarding claims 16-17, Deo teaches that the HaloCaMP comprises a CaM (i.e., a calmodulin) and a CaM-binding peptide (i.e., a calmodulin binding peptide), wherein there is at least one linker disposed between the CaM and CaM-binding peptide (pg. 720; see Fig. 2).
Regarding claim 20, Deo teaches that the HaloCaMP may be expressed within (i.e., contacted with) neuronal cells in order to detect calcium within the cells (i.e., the analyte of interest may be detected within the cell) (pg. 721).
Claim(s) 4-6 and 9-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Deo (Nature chemical biology 17.6 (1 April 2021): 718-723) in view of Frei (Nature methods 19.1 (16 December 2021): 65-70) as applied to claims 1-3, 13-17, and 20 above, and further in view of Deben (PG Pub No. US 2024/0133869 A1, filed 13 March 2022).
Regarding claims 4-6 and 9-12, Deo in view of Frei renders obvious claims 1-3, 13-17, and 20 as described above.
Deo in view of Frei does not teach or suggest that the SLP has the sequence of SEQ ID NO: 1, wherein 0 residues are removed from a terminus, and wherein there is 1 mutation between residues 145-180 (Claim 4).
Deben is drawn towards an invention concerned with methods for determining an effect of an active agent on a sample (Abstract). Deben teaches the use of a HaloTag polypeptide that has 100% identity to the claimed SEQ ID NO: 1 ([0206]; see SEQ ID NO: 2 in attached sequence alignment).
The applicable teachings and obviousness of introducing a mutation between residues 145-180 are discussed above as applied to claim 1.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the SLP such that it had the sequence of the claimed SEQ ID NO: 1, wherein there is 1 mutation between residues 145-180 and 0 residues are removed from a terminus, because it would have merely amounted to a simple substitution of one HaloTag polypeptide for another to yield predictable results. Since Deo and Frei teach using a tryptophan-modified HaloTag at position 175 as applied to claim 1, it would have been predictable to have similarly made and used a HaloTag comprising the claimed SEQ ID NO: 1 and a tryptophan-modification at position 175 in order to detect calcium when present within the HaloCaMP construct of Deo and Frei.
Regarding claims 5-6, Frei further teaches the use of a HaloTag7 that was mutated with a G171W mutation (i.e., a tryptophan-modification at residue 171 of the HaloTag polypeptide) (see Supplementary Figure 2 and Table S1). Frei teaches that the G171W mutant displayed a higher fluorescence polarization compared to the wildtype HaloTag (see Supplementary Figure 2).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have arrived at the requirements of the claimed SEQ ID NO: 1 comprising a tryptophan-modification at residue 171 because it would have merely amounted to a simple substitution of one HaloTag for another to yield predictable results. Since Deo and Frei teach using a tryptophan-modified HaloTag at position 171, it would have been predictable to have similarly made and used a HaloTag comprising the claimed SEQ ID NO: 1 and a tryptophan-modification at position 171 in order to detect calcium when present within the HaloCaMP construct of Deo and Frei. And because Frei teaches that the introduced G171 tryptophan modification resulted in a higher fluorescence polarization, one would have been motivated to do so.
Regarding claims 9 and 12, Deo teaches that a (GGTGGS)3 linker is inserted between the HaloTag C-terminus and N-terminus in order to facilitate the circular permutation of the HaloTag (pg. 720; see Fig. 2).
Regarding claim 10, Deo teaches that a (GGTGGS)3 circular permutation linker may be inserted at position 152 of the Halotag (i.e., resulting in an N-terminus that extends from residue 1 to residue 151 and a C-terminus that extends from residue 170-297 of the claimed SEQ ID NO: 1) (see Supplementary Figure 1).
Regarding claim 11, Deo teaches that the HaloTag is circularly permutated (pg. 720; see Fig. 2).
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 filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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/apply/applying-online/eterminal-disclaimer.
Claims 1 and 3 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of U.S. Patent No. 11,708,397 in view of Frei (Nature methods 19.1 (16 December 2021): 65-70).
Regarding claims 1 and 3, patented claim 1 claims “a chemigenetic calcium indicator, comprising:
(a) a calcium-binding protein domain [(i.e., an analyte sensing domain)],
(b) a ligand-binding protein domain attached to the calcium-binding protein domain [(i.e., an SLP)], and
(c) a fluorescent dye conjugated to a ligand for the ligand-binding protein domain;
wherein the calcium indicator comprises a polypeptide selected from the group consisting of SEQ ID NO: 2, 4, 6, 8, 10, and 12.”
Patented claim 2 claims that the ligand binding protein is a self-labeling protein.
Patented claims 1-2 do not teach or suggest that the SLP has a tryptophan-modification (Claim 1). Patented claims 1-2 do not teach or suggest that the tryptophan modification is within about 5 Å from the fluorescent dye (Claim 3).
The applicable teachings of Frei and Deo are discussed above as applied to claims 1 and 3.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention modify the SLP via the introduction of a tryptophan modification that is within about 5 Å from the fluorescent dye because it would have merely amounted to a simple combination of prior art elements according to known methods to yield predictable results. Because Frei and Deo teaches using a mutated HaloTag protein used for a similar purpose as the patented claims, namely the self-labeling of the HaloTag protein through the use of a fluorescent dye, then one would have had a reasonable expectation of success in mutating the HaloTag protein of Frei and Deo via the introduction of a tryptophan modification and maintaining the HaloTag’s ability to self-label with a fluorescent dye. And because Frei teaches that the introduced tryptophan modification resulted in a more photostable tag, one would have been motivated to do so.
Claims 2 and 13-17 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of U.S. Patent No. 11,708,397 in view of Frei (Nature methods 19.1 (16 December 2021): 65-70) as applied to claim 1 above, and further in view of Deo (Nature chemical biology 17.6 (1 April 2021): 718-723).
Regarding claims 2-3 and 13-17, patented claims 1-2 in view of Frei render obvious claims 1 and 3 as described above. Patented claim 1 claims the use of a calcium-binding protein (i.e., a protein that binds to a calcium analyte).
Patented claims 1-2 in view of Frei do not teach or suggest that the tryptophan modification is positioned relative to the ASD and, upon binding of the ligand to the SLP, the tryptophan modification migrates to quench or allow fluorescence when the ASD undergoes a confirmational change (Claim 2). Patented claims 1-2 in view of Frei do not teach or suggest that the ASD undergoes a confirmational change when it binds to an analyte (Claim 13). Patented claims 1-2 in view of Frei do not teach or suggest that there is a linker disposed between the calmodulin and calmodulin binding peptide (Claim 17).
The applicable teachings of Deo and Frei are discussed above as applied to claims 2, 13, and 17.
Therefore, the claimed invention is obvious for the same reasons discussed above as applied to claims 2, 13, and 17.
Regarding claims 14-15, patented claim 1 claims that the analyte is calcium.
Regarding claim 16, patented claim 5 claims that the calcium binding protein comprises calmodulin and a calmodulin binding peptide.
Claims 4-6 and 9-12 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of U.S. Patent No. 11,708,397 in view of Frei (Nature methods 19.1 (16 December 2021): 65-70) as applied to claims 1 and 3 above, and further in view of Deben (PG Pub No. US 2024/0133869 A1, filed 13 March 2022).
Regarding claims 4-6 and 9-12, patented claims 1-2 in view of Frei render obvious claims 1 and 3 as described above.
Patented claims 1-2 in view of Frei does not teach or suggest that the SLP has the sequence of SEQ ID NO: 1, wherein 0 residues are removed from a terminus, and wherein there is 1 mutation between residues 145-180 (Claim 4). Patented claims 1-2 in view of Frei does not teach or suggest that the tryptophan modification is between residues 145-176 (Claim 5) and is located at position 171 (Claim 6). Patented claims 1-2 in view of Frei does not teach or suggest that a linker is disposed between the N- and C-terminal portions of the SLP (Claim 9). Patented claims 1-2 in view of Frei does not teach or suggest that the N-terminal portion extends from residue 1-4 to residue 150-180 and the C-terminal portion extends from residue 151-181 to 294-297 (Claim 10). Patented claims 1-2 in view of Frei does not teach or suggest that the SLP is circularly permutated and comprises a linker disposed between the C-terminal and N-terminal portions (Claims 11-12).
The applicable teachings of Frei, Deo, and Deben are discussed above as applied to claims 4-6 and 9-12.
Therefore, the claimed invention is obvious for the same reasons discussed above as applied to claims 4-6 and 9-12.
Allowable Subject Matter
Regarding claims 7-8, the closest prior art is Frei (Nature methods 19.1 (16 December 2021): 65-70). Frei is drawn towards a study concerned with engineered HaloTag variants for fluorescence lifetime multiplexing (Abstract). Frei teaches the generation of HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines through the mutation of the HaloTag variants at specific amino acid positions in the proteins (Abstract)
However, Frei does not teach or suggest the claimed one additional mutation is present at a position selected from positions 157-158, 176, 178, and 180 (see Claim 7), wherein the mutations are selected from V157L, G158D, G176A, V178A, V178I, G178W, P180Y, P180T, and P180V (see Claim 8). Further Frei does not identify the additional mutational sites as regions of interest nor as sites that should be mutated.
Accordingly, the claimed chemigenetic indicator comprising the claimed additional mutations is both novel and non-obvious in view of the closest prior art.
Applicant has provided adequate written description support for the additional mutations and provides evidence that, when combined with a tryptophan-modification at positions 151 or 171, the resulting chemigenetic indicators displayed improved responses compared to chemigenetic sensors that did not have the additional claimed mutation ([0066]; see Table 1A).
Accordingly, Applicant has provided adequate written description support for the claimed chemigenetic indicators comprising the claimed additional mutations. Further, Applicant has provided novel and non-obvious evidence that the additional mutations at the claimed sites provide a beneficial effect to the claimed chemigenetic indicators.
Therefore, claims 7-8 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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