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 1-6) in the reply filed on 12/4/25 is acknowledged. The traversal is on the ground(s) that Group I is basically the same as that of Group II and III, and any prior art searched for one group is applicable to the other group, and hence there would not be a serious search and/or examination burden. This is not found persuasive because prior art searched for Group I is not necessarily applicable to Group II or III. For example, Group I requires the following, which is not required by Group III: identifying a fragmentation site in a signal-generating protein using sequence dissimilarity analysis, splitting the signal-generating protein at the fragmentation site, and mutating a residue on one or both of the protein fragments. Group III which requires the following, which is not required by Group I: a step of detecting a signal when a first protein and a second protein interact, causing a first protein fragment and a second protein fragment to associate, thereby reassembling the protein fragments into a signal-generating protein that exhibits the detectable signal. Examiner notes that upon finding allowable subject matter, potential rejoinder of claims would be considered.
The requirement is still deemed proper and is therefore made FINAL.
Claims 7-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 12/4/25.
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 1-6 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.
Claim 1, lines 2-3 recites “a) identifying a fragmentation site in a signal-generating protein using sequence dissimilarity analysis”. However, it is not clear as to what comprises a “sequence dissimilarity analysis”. Examiner notes that while a claim is interpreted in light of the specification, the specification is not read into the claims unless the specification provides a clear meaning or definition to a claimed limitation. Applicant’s specification discloses what may be considered “sequence dissimilarity” (para. 0046), and gives examples of a sequence dissimilarity analysis (paras. 0077, 0080, 0081). But such examples do not give a clear meaning or definition to “sequence dissimilarity analysis” as they are varied and are merely examples. Clarification is requested. For examination purposes, the limitation is interpreted to encompass any technique that results in identifying a fragmentation site in a signal-generating protein.
Claims 2-6 are rejected since they depend from claim 1 without clarifying the vagueness discussed above.
.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-5 is/are rejected under 35 U.S.C. 102(a)as being anticipated by US 20090170069 (hereinafter “Ghosh”).
Ghosh discloses the limitations of Applicant’s claims as follows.
Regarding claim 1, Ghosh discloses a method of preparing a split signal-generating protein, comprising:
identifying a fragmentation site in a signal-generating protein using sequence dissimilarity analysis
[see para. 0151 disclosing that “[g]enerally, split-protein reassembly or protein complementation utilizes a protein reporter dissected into two inactive fragments, each of which when appended to a member of an interacting protein/peptide pair results in reassembly of the dissected protein reporter whose activity can be measured];
splitting the signal-generating protein at the fragmentation site to produce a first protein fragment and a second protein fragment
[see para. 0151 disclosing that “[g]enerally, split-protein reassembly or protein complementation utilizes a protein reporter dissected into two inactive fragments, each of which when appended to a member of an interacting protein/peptide pair results in reassembly of the dissected protein reporter whose activity can be measured];
and c) mutating at least one residue in one or both of the protein fragments
[see para. 0012 disclosing “[a] fuorescent protein be a naturally occurring or engineered or enhanced green, blue, yellow, red or other fluorescent protein. A green fluorescent protein or variant can be one derived in sequence from or modified from Aequoria, or Discosoma. Luciferase can be one derived in sequence from or modified from firefly” (emphasis added)]
[see para. 0013 disclosing addition of unnatural amino acids used in translation, for example, amino acid analogues, with tRNAs charged with natural and/or unnatural amino acids, as desired; and disclosing that “the art knows the appropriate vector and sequence modifications for the system in which the split reporter(s) are produced]
[see para. 0161 disclosing that “[b]oth split-GFP and split-β-lactamase were rationally designed, such that the point of dissection and new-protein attachment sites lie between the loops].
Regarding claim 2, Ghosh discloses that the method further comprises:
a) connecting the first protein fragment to a first protein of a protein-protein interaction via a first linker to form a first sensor complex
[see para. 0007 disclosing assays for detecting protein-protein interactions];
and b) connecting the second protein fragment to a second protein of the protein-protein interaction via a second linker to form a second sensor complex
[see para. 0007 disclosing that two portions of the reporter protein come together in a cell-free assay and their association is mediated by an interaction of an attached protein and its specific ligand, which can be an antibody or other protein, etc.]
[see para. 0007 also disclosing that protein-ligand and protein-small molecule interactions can be assessed when at least one portion of the reporter protein is covalently or noncovalently linked to either a ligand or to an antagonist or agonist of a bimolecular interaction and the second, complementing portion of the reporter protein is expressed in a cell-free translation system];
wherein the split-protein sensor comprises the first and second sensor complexes.
[see para. 0007 disclosing interaction of the two binding partners, with either their ligands or each other, brings the two portions of the split reporter protein into sufficiently close proximity that the two portions reassemble into a functional protein with detectable activity]
[see paras. 0024-0025, 0046, disclosing protein-protein interactions interrogated by bioluminescence, fluorescence, or luciferases].
Regarding claim 3, Ghosh discloses that the method generates a split-protein sensor for detecting protein-protein interactions
[see para. 0007 disclosing that two portions of the reporter protein come together in a cell-free assay and their association is mediated by an interaction of an attached protein and its specific ligand, which can be an antibody or other protein, etc.]
[see para. 0007 also disclosing that protein-ligand and protein-small molecule interactions can be assessed when at least one portion of the reporter protein is covalently or noncovalently linked to either a ligand or to an antagonist or agonist of a bimolecular interaction and the second, complementing portion of the reporter protein is expressed in a cell-free translation system;
interaction of the two binding partners, with either their ligands or each other, brings the two portions of the split reporter protein into sufficiently close proximity that the two portions reassemble into a functional protein with detectable activity]
[see paras. 0024-0025, 0046, disclosing protein-protein interactions interrogated by bioluminescence, fluorescence, or luciferases].
Regarding claim 4, Ghosh discloses that the signal-generating protein is a luminescent protein
[see para. 0007 disclosing reporter systems generating, for example, bioluminescence, chemiluminescence, fluorescence, for example using luciferase, beta-lactamase or a fluorescence protein reporter system; wherein two portions of the reporter protein come together in a cell-free assay and their association is mediated by an interaction of an attached protein and its specific ligand, which can be an antibody or other protein, etc.]
[see para. 0007 also disclosing that interaction of the two binding partners, with either their ligands or each other, brings the two portions of the split reporter protein into sufficiently close proximity that the two portions reassemble into a functional protein with detectable activity]
[see para. 0059 disclose that the “cell-free assay can employ a variety of split protein reporters to provide fluorescent (β-lactamase) or bioluminescent (luciferase) signal out puts”].
Regarding claim 5, Ghosh discloses mutating at least one residue comprises replacing said residue with another amino acid
[see para. 0012 disclosing “[a] fuorescent protein be a naturally occurring or engineered or enhanced green, blue, yellow, red or other fluorescent protein. A green fluorescent protein or variant can be one derived in sequence from or modified from Aequoria, or Discosoma. Luciferase can be one derived in sequence from or modified from firefly” (emphasis added)]
[see para. 0013 disclosing addition of unnatural amino acids used in translation, for example, amino acid analogues, with tRNAs charged with natural and/or unnatural amino acids, as desired; and disclosing that “the art knows the appropriate vector and sequence modifications for the system in which the split reporter(s) are produced].
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) 6 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 20090170069 (hereinafter “Ghosh”).
Ghosh, discussed above, is silent as to the signal-generating protein has a signal to background ratio that is greater than 200.
However, providing signal to background ratio that is greater than 200 appears to fall within a workable or optimum range, and given that the general conditions of the claims are taught by Ghosh, its discovery would have required routine skills in the art.
See also paragraph 0124 in Ghosh disclosing detectable signal above background when the first and second fragments of the reporter associate.
See paragraph 0137 that following incubation of the split-Fluc constructs with the guide-target complex, a significant signal over background was observed.
See also paragraph 0145 in Ghosh disclosing that the designed ZF-modified split-Fuc constructs resulted in a signal of 4.5 fold as compared to background.
Given the teachings of Ghosh of the various ways of producing the split protein [see discussion of claim 1 above], and the desirability of increasing the signal as compared to the background [i.e., signal to background ratio] providing signal to background ratio that is greater than 200 would have required routine skills in the art.
Conclusion
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/Ann Montgomery/Primary Examiner, Art Unit 1678