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 .
Application Status
This action is written in response to applicant’s correspondence received on 21 July 2026. Claims 2-3 and 6-20 are currently pending. Claims 18-19 are withdrawn from prosecution as being drawn to non-elected subject matter. Accordingly, claims 2-3, 6-17, and 20 are examined herein. The restriction requirement mailed 9 February 2026 is still deemed proper. Applicant elected the species of analyte of claims 14-17 without traverse in the reply filed 10 March 2026. Accordingly, claims 2-3 and 6-20 are examined herein.
Any rejection or objection not reiterated herein has been overcome by amendment.
Applicant' s amendments have been thoroughly reviewed and are persuasive to place the
claims in condition for allowance for the reasons that follow. Because the newly recited rejections of record were not necessitated by amendment, this action is NON-FINAL.
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 2-3, 6-17, and 20 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.
Regarding claim 7, it is not clear how the residues recited by the claim relate to SEQ ID NO 1. It is unclear if the claimed positions in part (b) refer to positions within SEQ ID NO 1 or positions within the fusion protein comprising the ASD and the SLP. If the claimed positions refer to a tryptophan modification in SEQ ID NO 1, because there are no tryptophans in the claimed residues of SEQ ID NO 1, it’s not clear how the SLP can have the sequence of SEQ ID NO 1 but also have a tryptophan modification between residues 145-176. The claim further refers to the presence of mutations between positions 145 and 180 in part (c) of the claim. It’s not clear if these are referring to the positions within SEQ ID NO 1 or the positions within the broader fusion protein between the ASD and the SLP. It’s further not clear how the mutations between positions 145-180 relate to the tryptophan modification previously recited by the claim. Additionally, since SEQ ID NO 1 doesn’t have a tryptophan between residues 145 and 180 of SEQ ID NO 1, it’s not clear if this limitation in the claim is referring to a tryptophan insertional mutation or some other mutation. The claim further refers to additional mutations at residues 157, 158, 176, 178,and 180. It’s not clear whether these are referring to residues within SEQ ID NO 1 or residues in the fusion protein between ASD and SLP.
Additionally, it is also not clear how the removal of the residues at the N terminus or C terminus relates to the ASD, the SLP, the ligand, and SEQ ID NO 1. It’s not clear if the removal refers to the removal of residues of SEQ ID NO 1 or the fusion protein comprising the ASD and the SLP. If the removals are referring to the claimed SEQ ID NO: 1, it’s not clear how the SLP can both have residues removed from SEQ ID NO 1 but also have the sequence of SEQ ID NO 1.
Regarding claims 2-3, 6, 8-17, and 20, as the claims are ultimately dependent on claim 7 and do not rectify the 35 USC 112(b) rejection above, the claims are also rejected under 35 USC 112(b).
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 2-3, 6-17, and 20 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.
Regarding claim 7, for the purposes of examination the claimed mutations are interpreted as referring to amino acid positions within the claimed SEQ ID NO: 1. Additionally, the claimed 1 mutation between residues 145-180 is interpreted as being the same thing as the claimed tryptophan modification between residues 145-176. Additionally, the claimed tryptophan modification is interpreted as encompassing an introduction of a tryptophan at the claimed residue.
The claim is directed towards a chemigenetic fluorescent indicator that can detect an analyte of interest comprising an extraordinarily broad genus of mutations selected from a tryptophan modification between residues 145-176 of the SLP, wherein there are 1, 2, 3, 4, or 5 mutations between residues 145-185, and wherein there is at least one additional mutation at a residue selected from the group consisting of 157, 158, 176, 178, and 180 (see Claim 7).
Accordingly, the claims are interpreted as reciting a genus of mutations that possess the claimed function of being able to identify an analyte when present within the claimed chemigenetic indicator.
The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include "level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would leave one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP 2163. A claimed genus may be satisfied through sufficient descriptions of a representative number of species or disclosure of relevant, identifying characteristics such as functional characteristics coupled with known or disclosed correlation between function and structure. MPEP 2163(3)a(II). The number of species that describe the genus must be adequate to describe the entire genus; if there is substantial variability, a large number of species must be described.
The analysis for adequate written description considers (a) actual reduction to practice, (b) disclosure of drawings or structural chemical formulas, (c) sufficient relevant identifying characteristics in the way of complete/partial structure or physical and/or chemical properties or functional characteristics when coupled with known or disclosed correlation with structure, and (d) representative number of samples.
As the claims currently recite, as described above, the claim is directed towards a chemigenetic fluorescent indicator that can detect an analyte of interest comprising an extraordinarily broad genus of mutations selected from a tryptophan modification between residues 145-176 of the SLP, wherein there are 1, 2, 3, 4, or 5 mutations comprising any amino acid between residues 145-185, and wherein there is at least one additional mutation comprising any amino acid at a residue selected from the group consisting of 157, 158, 176, 178, and 180. While claiming a structure by a function is not prohibited, there must be sufficient structure-function relationship described in the specification such that the claimed genus was represented by a representative number of species or the teachings of the specification, or, the prior art can be used support a well-known structure-function relationship.
In the instant case, the instant specification does not support the claimed structure-function relationship that mutating all of the claimed mutational positions with any possible amino acid would predictably result in the determination of an analyte of interest. Further, the prior art does not support a clear, well-defined, and predictable structure-function relationship between any mutation at any of the claimed mutational sites and having the function of being able to detect an analyte of interest.
Prior Art
Prior to the effective filing date of the claimed invention, the prior art provides evidence that mutating an SLP in order for it to be used within a chemigenetic fluorescent indicator must be done within specific mutational sites present within close proximity to a bioavailable dye in order to detect an analyte.
Regarding the state of the art surrounding mutational analysis of HaloTag (i.e., SLP) mutants, Frei (Nature methods 19.1 (16 December 2021): 65-70) is drawn towards a study concerned with engineered HaloTag variants for fluorescence lifetime multiplexing (Abstract). Frei teaches that there is a need in the art to generate HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines in order to modulate the brightness and fluorescence lifetime of bound rhodamines (i.e., fluorescent dyes) for use in live-cell fluorescence lifetime multiplexing (Abstract) Frei teaches the use of a HaloTag variant, termed HaloTag11, that comprises an M175W mutation (i.e., a tryptophan modification at residue 175) (pg. 65). Frei teaches that the analysis of the introduction of different amino acids at positions M175, V167, E170, T148, L161, Q165, T172, F144, G171, P174, alongside combinations of two or three of the mutational positions, was a known method of determining if the mutation resulted in a higher or lower brightness and fluorescence lifetime compared with HaloTag7 (see Supplementary Table S1). Frei teaches that the ten mutational sites were selected because they were present on helices 6–8 of the HaloTag polypeptide in close proximity to fluorescent TMR (i.e., a rhodamine dye) when it was bound to the polypeptide (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).
Thus, the closest prior art teaches that it was neither predictable nor well-known that any number of mutations present within the claimed range of mutations, wherein the mutations are any amino acid possessed the function of being able to identify an analyte of interest when present within an SLP. Rather, the closet prior art shows that the mutational sites must be present within a specific proximity to the dye and present within specific helices in order to detect the dye.
Therefore, the prior art does not support a clear, well-defined, and predictable structure-function relationship between the extraordinarily broad genus of mutations selected from a tryptophan modification between residues 145-176 of the SLP, wherein there are 1, 2, 3, 4, or 5 mutations selected from any amino acid between residues 145-185, and wherein there is at least one additional mutation selected from any amino acid at a residue selected from the group consisting of 157, 158, 176, 178, and 180 and the function of being able to identify an analyte of interest.
Working Examples
With regard to working examples, the specification provides little evidence on the possession of a sufficient number of species which are encompassed by the claimed genus and possess the claimed function. The instant specification identifies a total of two different tryptophan modifications, G171W and A151W, that could be present within SEQ ID NO: 1 and combined with other mutations in order to generate different functional indicators (pg. 13-14; see Table 1A). The instant specification teaches that within the SEQ ID NO: 1 comprising the G171W mutation, the tested mutational sites that could generate a functional indicator were G176A, V178A, P180Y, G176A, V178I, and P180T (pg. 13-14; see Table 1A). The instant specification teaches that within the SEQ ID NO: 1 comprising the A151W mutation, the tested mutational sites that could generate a functional indicator was G158D (pg. 13-14; see Table 1A).
The instant specification has not identified any additional tryptophan modification sites that could be present within the claimed SEQ ID NO: 1 nor additional mutational sites that could be combined with the tryptophan modifications in order to generate a functional indicator. At most, the instant specification appears to describe 7 different total species of indicators that could perform the claimed function. Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would recognize that the instant specification does not provide written description for the entirety of the claimed genus of mutations selected from a tryptophan modification between residues 145-176 of the SLP, wherein there are 1, 2, 3, 4, or 5 mutations selected from any amino acid between residues 145-185, and wherein there is at least one additional mutation selected from any amino acid at a residue selected from the group consisting of 157, 158, 176, 178, and 180 and the function of being able to identify an analyte of interest.
Conclusion
The specification does not identify a structure-function relationship between the claimed mutations and the function of being to identify an analyte of interest sufficient to show the applicant was in possession of the claimed genus. Further, the closet prior art shows that prior to the effective filing date of the claimed invention that the mutational sites must be in a specific region of the SLP in order to be able to detect an analyte of interest. Taken together, the skilled artisan would not have reasonably concluded at the time of the invention that applicant was in possession of the invention as claimed. Thus, claim 7 is rejected under 35 U.S.C. 112(a).
Regarding claim 8, the claim further limits the additional mutation to specific amino acids. However, for the same reasons described above the claim is rejected under 35 USC 112(a) because the claim broadly encompasses a genus of mutations selected from a tryptophan modification at any position between residues 145-176 of the SLP, wherein there are 1, 2, 3, 4, or 5 mutations selected from any amino acid between residues 145-185, and posing the function of being able to identify an analyte of interest. The recitation of specific additional mutations does not rectify the broadly recited genus of tryptophan modifications, nor the 1-5 mutations selected from any amino acid between residues 145-185 of the SLP.
Regarding claims 2-3, 6, 9-17, and 20, as they are ultimately dependent on claim 7 and do not rectify the written description rejection described above, the claims are also rejected under U.S.C. 112(a).
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) 2-3, 6-17, 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 Deben (PG Pub No. US 2024/0133869 A1, filed 13 March 2022) and Frei (Nature methods 19.1 (16 December 2021): 65-70).
Regarding claim 7, for the purposes of examination the claimed 1 mutation between residues 145-180 is interpreted as being the same thing as the claimed tryptophan modification between residues 145-176. Additionally, the claimed tryptophan modification is interpreted as encompassing an introduction of a tryptophan at the claimed residue.
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 between residues 145-176 (i.e., 1 mutation between residues 145-180) (Claim 1). Deo 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 one additional mutation at a residue selected from the group consisting of 157, 158, 176, 178, and 180 (Claim 7).
Regarding the state of the art surrounding mutational analysis of HaloTag mutants, Frei is drawn towards a study concerned with engineered HaloTag variants for fluorescence lifetime multiplexing (Abstract). Frei teaches that there is a need in the art to generate HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines in order to modulate the brightness and fluorescence lifetime of bound rhodamines for use in live-cell fluorescence lifetime multiplexing (Abstract) Frei teaches the use of a HaloTag variant, termed HaloTag11, that comprises an M175W mutation (i.e., a tryptophan modification at residue 175) (pg. 65). Frei teaches that the analysis of the introduction of different amino acids at positions M175, V167, E170, T148, L161, Q165, T172, F144, G171, P174, alongside combinations of two or three of the mutational positions, was a known method of determining if the mutation resulted in a higher or lower brightness and fluorescence lifetime compared with HaloTag7 (see Supplementary Table S1). Frei teaches that the ten mutational sites were selected because they were present on helices 6–8 of the HaloTag polypeptide in close proximity to fluorescent TMR (i.e., a rhodamine dye) when it was bound to the polypeptide (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).
Deben is drawn towards an invention concerned with methods for determining an effect of an active agent on a sample through the use of a luminescent cell-death marker (Abstract). Deben teaches the use of a luminescent cell-death marker fusion protein that comprises a HaloTag polypeptide, wherein the HaloTag polypeptide has 100% identity to the claimed SEQ ID NO: 1 ([0206]; see SEQ ID NO: 2 in previously attached sequence alignment).
Therefore, regarding the claimed SEQ ID NO: 1, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the HaloTag polypeptide of Deo for the HaloTag polypeptide of Deben because it would have merely amounted to a simple substitution of one HaloTag polypeptide for another to yield predictable results. Because both references teach that HaloTag polypeptides (i.e., polypeptide with the same function) can be utilized in fusion proteins, one would have expected utilizing the Halotag polypeptide of Deben within the chemigenetic fluorescent indicator of Deo to have successfully resulted in the generation of a HaloCaMP that can detect the presence of an analyte.
Additionally, regarding the claimed tryptophan modification and 1 mutation within the claimed residue range, 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 HaloCaMP rendered obvious by the combination of Deo and Deben via the introduction of an M175W mutation 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.
Finally, regarding the presence of at least one claimed additional mutation at position 157, 158, 176, 178, and 180, alongside the claimed specific amino acids present in claim 8, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have tried to modify the HaloCaMP rendered obvious by the combination of Deo and Deben via the introduction of at least one mutation at the claimed sites. Frei teaches that there was a need to generate HaloTag variants with either increased or decreased fluorescence intensity, demonstrating that there had been a recognized problem or need in the art to mutate HaloTag polypeptides. Frei teaches that the possible amino acids of interest that could be mutated were present on helices 6–8 of the HaloTag polypeptide in close proximity to fluorescent TMR (i.e., a rhodamine dye) when it was bound to the polypeptide (i.e., Frei teaches that there had been a finite number of potential additional mutational sites of the HaloTag polypeptide that were near the studied ten mutational sites and within proximity to the dye). Frei also discloses extensive mutational analysis at positions M175, V167, E170, T148, L161, Q165, T172, F144, G171, P174, alongside combinations of two or three of the mutational positions, with the additional analysis of determining if the resulting HaloTag polypeptide had increased or decreased fluorescence intensity compared to an unmutated HaloTag polypeptide (i.e., Frei teaches that one of ordinary skill in the art could have pursued different mutations at different mutational sites present on helices 6-8 with a reasonable expectation of success). Thus, it would have been obvious for a person of ordinary skill in the art to have tried to mutate the claimed additional mutational sites and selected specific amino acids that altered the properties of the HaloTag’s florescence in order to generate an indicator that could detect an analyte of interest.
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 claim 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).
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).
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).
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 2-3, 6-17, and 20 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 Deo, Deben, and 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 claims 1-2 do not teach or that the SLP has a tryptophan-modification between residues 145-176 (i.e., 1 mutation between residues 145-180) (Claim 7) or located at position 171 (Claim 6). Patented claims 1-2 do 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 one additional mutation at a residue selected from the group consisting of 157, 158, 176, 178, and 180 (Claim 7). Patented claims 1-2 do not teach or suggest that the tryptophan modification is within about 5 Å from the fluorescent dye (Claim 3). Patented claims 1-2 do 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 do 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 do 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 Deo, Deben, and Frei are discussed above as applied to claim 7.
Regarding the use of the claimed SEQ ID NO: 1, the applicable obviousness rationale is discussed above as applied to claim 7.
Regarding the claimed tryptophan modification, the applicable obviousness rationale is discussed above as applied to claim 7.
Regarding the claimed additional mutation, the applicable obviousness rationale is discussed above as applied to claims 7-8.
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 claim 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).
The applicable obviousness rationale describing including a tryptophan medication within the claimed SEQ ID NO: 1 is discussed above as applied to claims 6-8. Therefore, it would have been obvious to one of ordinary skill in the art to have included a G171W mutation within the claimed SEQ ID NO: 1.
Regarding claims 9-12, 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). Deo teaches that the (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).
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 copending indicator such that it was circularly permutated through the use of the (GGTGGS)3 circular permutation linker because it would have merely amounted to a combination of prior art elements according to known methods to yield predictable results. Because both the copending claims and the combination of Deo, Deben, and Frei teach that HaloTags can be linked to a calcium-binding protein domain in order to generate a calcium indicator, one would have expected utilizing the circular permutation linker within the copending claims to have resulted in a functional indicator. Additionally, because Deo teaches that circular permutation allows for the sensor domain to be in close proximity to the chromophore, one would have been motivated to have done so.
Regarding claim 13, 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 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.
Regarding claim 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, patented claim 13 claims a method of measuring calcium, the method comprising administering the chemigenetic calcium indicator of claim 1 and determining changes in fluorescence.
Conclusion
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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