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 .
Status of the Application
The Amendment and Response filed January 21, 2026 is acknowledged.
Claims 2-4, 8-9, 12-17 and 23-32 were pending. Claims 2-4, 8-9, 12-17, 23-29 and 31-32 are being examined on the merits. Claim 30 remains withdrawn.
Response to Arguments
Applicant’s arguments filed January 21, 2026 have been fully considered.
The following rejections are WITHDRAWN in view of Applicant’s arguments and amendments to the claims:
Rejection of claim 25 under 35 USC § 112(b), indefiniteness
The following rejections are MAINTAINED:
Prior art rejection of claim 29
Response to arguments regarding prior art rejections
Applicant argues that the prior art rejection of claim 29 should be withdrawn because Ali was cited for teaching that the capture ligand and the reporter molecule can be placed on different molecules in the detection complex, but Applicant cannot determine where and how Ali allegedly teaches this, and thus has not been given proper notice as to the rationale behind the rejection (Remarks, p. 8).
The Examiner disagrees. Ali clearly shows, e.g., in the abstract figure and in Fig. 1, a detection complex where biotin is attached to the Cas9 molecule, while the FAM reporter molecule is attached to amplified target DNA. Thus, the “capture ligand” and “reporter molecule” are “placed on different molecules in the detection complex” as compared to the Marsic detection complex, as stated in the Non-Final Office Action mailed October 22, 2025 (p. 9). This embodiment is further discussed throughout the entire the reference. Since Applicant surely reviewed Ali and would obviously understand that, the source of Applicant’s confusion is unclear to the Examiner. Perhaps Applicant is asserting that the terms “reporter molecule” and “capture ligand” in claim 29 are intended to be construed so narrowly that they are not analogous to the Ali biotin and FAM components? Or perhaps the claim 29 composition is assembled in a manner that is inconsistent with the Ali detection complex? It is noted that the instant specification does not define any of the terms “reporter molecule”, “capture ligand” or “probe”. Nevertheless, in an attempt to advance prosecution, the rejection has been modified to include additional details.
Applicant additionally argues that the rejection should be withdrawn because the Non-Final Office Action mailed October 22, 2025 stated both that the configuration of the detection complex itself could have been arrived at through routine optimization, while also stating that there would not have been a reasonable expectation of success of using a biotinylated gRNA molecule in the Marsic detection method to detect the target nucleic acid. Applicant argues that these positions are inconsistent (Remarks, pp. 9-10).
The Examiner disagrees. The positions are not inconsistent, and this issue has been previously raised and addressed. Specifically, the Examiner refers Applicants to the statements in the Non-Final Office Action mailed October 22, 2025 (p. 4), which states that there would not be at least a reasonable expectation of success in modifying the Marsic method to swap the positions of the capture ligand and the reporter moieties in the detection complex. Stated differently, if the ordinary artisan did modify Marsic to swap the positions of those moieties, there would not be a reasonable expectation of success that the Marsic method would still work as intended. However, in a standalone product claim, as in instant claim 29, the detection complex doesn’t have to work in the corresponding Marsic method. It could be used in a different method, or it could be made for some other reason altogether. Further, generally speaking, rearranging parts of compositions is obvious. MPEP 2144.04(VI)(C). So, in the instant product claims, it is obvious to swap the positions of the capture ligand and the reporter molecules, but in the method claims, it is not obvious because such a modified detection complex would not reasonably be expected to work in that particular method.
The rejections are maintained.
Allowable Subject Matter
The indicated allowability of claims 2-4 is withdrawn in view of a reconsideration of MPEP 608.01(n)(III), which states, in part, that “a claim in dependent from shall contain: (i) a reference to a claim previously set forth …”. The indicated allowability of claims 2-4, 8-9, 12-17, 23-29 and 31-32 is withdrawn in view of a reconsideration of certain issues under 35 USC § 112(b), indefiniteness.
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 4, 8-9, 12-17, 23-29 and 31-32 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 8 recites the limitation “the molecule is capable of … enhancing the kinetics of
hybridization”, the meaning of which is unclear. The specification does not define the limitation1, nor does it have a fixed meaning in the art. In addition, while the limitation “… capable of localizing a single-stranded nucleic acid strand to a double-stranded nucleic acid” is not indefinite in and of itself, it is not clear what the distinction is between the “capable of localizing …” limitation and the “enhancing the kinetics …” limitation. While the specification and claims 2-3 describe various embodiments of the “molecule” that meet such limitations (e.g., CRISPR-Cas proteins in claim 2), to the extent that claim 8 is directed to embodiments that do not comprise the “molecules” in claims 2-3, it is unclear what molecules or what structural components of molecules would be “capable of … enhancing the kinetics …” and how these molecules or structural components would differ from those that that are “capable of localizing …”. Claims 29 and 32 recite the same limitation, and are rejected with corresponding reasoning.
Claims 4, 9, 12-17, 23-28 and 31 depend directly or indirectly from claim 8 and consequently incorporate the indefiniteness issue of claim 8.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2-4 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Each of claims 2-4 depend from claim 8. Since each of claims 2-4 do not depend from a
claim previously set forth, they are in improper dependent form. See MPEP 608.01(n)(III).
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Interpretation
12. Applicant did not define the term “probe”, therefore any oligonucleotide is considered to anticipate this term.
13. Applicant did not define the term “reporter molecule”, therefore any molecule which can be detected is considered to anticipate this term.
14. Applicant did not define the term “capture ligand”, therefore any molecule which can be captured by any other molecule is considered to anticipate this term. Further, reporter molecules can also serve as capture ligands.
15. Applicant did not define the term “capture probe”, therefore any molecule which binds to another molecule is considered to anticipate this term.
16. Applicant did not define the term “capture label”, therefore any molecule which binds to another molecule is considered to anticipate this term.
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.
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 29 is rejected under 35 U.S.C. 103 as being unpatentable over Marsic2 et al. (Nano Letters, vol. 21, pp. 3596-3603, 2021) in view of Qiao3 et al. (Front. Chem., 9:786354, pp. 1-17, 2021), Awwad4 et al. (MethodsX, vol. 7, pp. 1-8, 2020) and Ali5 (Bio-SCAN: A CRISPR/dCas9-Based Lateral Flow Assay for Rapid, Specific, and Sensitive Detection of SARS-CoV-2, ACS Synth. Biol., 11, 406-419, 2021).
Regarding claim 29, Marsic et al. teach a composition comprising:
a probe and a double-stranded or single-stranded amplicon from amplification of a target nucleic acid, wherein the probe comprises a first nucleic acid strand and a molecule bound with the first nucleic acid strand, wherein the molecule is capable of localizing a single-stranded nucleic acid strand to a double-stranded nucleic acid or enhancing the kinetics of hybridization between two single-stranded nucleic acids, and wherein the first nucleic acid strand comprises a binding domain comprising a nucleotide sequence substantially complementary to at least a first portion of the amplicon (Abstract figures; Fig. 1; page 3597, last paragraph; page 3598).
Marsic additionally teaches that the amplicon and the first nucleic acid strand each comprise a moiety, and where the moieties are selected from a reporter molecule capable of producing a detectable signal, and a capture ligand (i.e. biotin) attached to the 3’ end of either the amplicon of the first nucleic acid strand (Abstract figures; Fig. 1; page 3597, last paragraph; page 3598; p. 3598, left col., para. 1 through right col., para. 1).
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However, Marsic does not teach that the moiety … is linked (directly) to the 3’ end of the first nucleic acid strand. However, Qiao and Awwad teach these limitations. Specifically, Qiao teaches that a moiety is linked directly to a first nucleic acid strand in a CRISPR-Cas9-based imaging system, but is silent as to the position of the moiety on the nucleic acid strand (Fig. 3C; pages 4-5: Section 3.3). In addition, Awwad teaches 3’ end labeling of noncoding RNAs with a variety of moieties (e.g., abstract; p. 2, para. 2).
Marsic also does not teach the specific embodiment where the amplicon is linked to a reporter molecule capable of producing a detectable signal, and the first nucleic acid strand is linked to a capture ligand (i.e. biotin). However, it would have been obvious to try different arrangements of molecules and moieties, as Ali teaches that the capture ligand and the reporter molecules can be placed on different molecules in the detection complex.
Specifically, Ali teaches, e.g., in the abstract figure and in Fig. 1, a detection complex where biotin is attached to the Cas9 molecule, while the FAM reporter molecule is attached to amplified target DNA. Thus, the “capture ligand” and “reporter molecule” are placed on different molecules in the detection complex as compared to the Marsic detection complex. It is also noted that the Ali reference is later work from the same group as the Marsic reference, and Ali discusses the Marsic VirD2-dCas9 detection complex and states that the Ali detection complex has been modified as compared to the Marsic detection complex by, in part, changing the position of the detectable labels (p. 407, right col., para. 1 through p. 408, left col., para. 1).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the Marsic detection complex by attaching the capture ligand to the 3’ end of first nucleic acid strand, and by attaching the reporter molecule to the amplicon. Marsic teaches the need for sensitive and specific point-of-care tests that are capable of detecting a variety of infectious diseases, using a detection complex labeled with multiple moieties. Qiao and Awaad teach various labeling protocols and Ali teaches that the moieties in the Marsic detection complex can be re-arranged on the various molecules comprised within the detection complex. Thus, the ordinary artisan would have been motivated to optimize the positioning of the moieties in the Marsic detection complex through routine experimentation with the expectation that doing so would result in a cost-effective and sensitive detection complex capable of detecting a desired target. In addition, rearranging parts of compositions is generally considered obvious. MPEP 2144.04(VI)(C). The ordinary artisan would have had an expectation of success as labeling nucleic acids with various moieties is well-known in the art.
Prior Art
Claim 8 is free of the art. Claim 8 requires, in part, that the amplicon comprises a reporter molecule and the first nucleic acid strand comprises a capture ligand. As noted in the prior art rejections, Marsic teaches the amplicon comprising a biotin/capture ligand, and the first nucleic acid strand/gRNA comprising FAM/reporter. Thus, instant claim 8 requires reversing these two moieties, which would require modifying the Marsic detection complex so that the amplicon comprises FAM and the gRNA comprises biotin. While rearranging parts is generally obvious, it does not appear to be the case in the Marsic method that it would be obvious to make such a rearrangement. That is, it is not clear that there would be a reasonable expectation of success that, in a modified Marsic detection complex, a gRNA comprising a biotin moiety would efficiently bind to the streptavidin on the LFA substrate while the gRNA and dCas9 complex was simultaneously bound to the amplicon, and at the same time the FAM-labeled amplicon would be able to bind to the detector antibody.
Specifically, Ali (Bio-SCAN: A CRISPR/dCas9-Based Lateral Flow Assay for Rapid, Specific,
and Sensitive Detection of SARS-CoV-2, ACS Synth. Biol., 11, 406-419, 2021) teaches an updated version of the Marsic assay where the amplicon is labeled with FAM. However, the biotin label is not attached to the gRNA itself, but rather the dCas9 protein. Ali teaches that they rearranged the assay components this way because doing so added simplicity, and improved sensitivity and specificity (p. 408, left col., para. 1).
In addition, Slesarev (CRISPR/Cas9 targeted CAPTURE of mammalian genomic regions for characterization by NGS, Scientific Reports, 9:3587, 1-12, 2019) teaches using CRISPR/Cas9 protocols for the targeted capture of genomic DNA regions of interest. In particular, Slesarev teaches the RGEN-D protocol (Fig. 2), where a 3’-biotinylated sgRNA and an inactive Cas9 protein complex with fragmented genomic DNA. The RGEN-DNA complexes are then isolated using streptavidin coated beads (Fig. 2). However, Slesarev teaches that the RGEN-D protocol is much less efficient at capturing the genomic DNA complexes on a substrate as compared to other methods that do not utilize a 3’-biotinylated sgRNA (Table 2).
Thus, given the concern about sensitivity in LFA assays (e.g., Marsic: abstract; Ali: abstract), it does not seem that the ordinary artisan would have had a reasonable expectation of success of using a biotinylated gRNA molecule in the Marsic detection complex and being able to bind enough detection complex to the substrate to detect the target nucleic acid. Claim 8 is thus free of the art.
Claims 2-4, 9, 12-17, 23-28 and 31-32 which depend from or otherwise incorporate the subject matter of claim 8 and are also free of the art.
Conclusion
Claims 2-4, 8-9, 12-17, 23-29 and 31-32 are being examined, and are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 The specification does define “enhancing” at para. 284.
2 Marsic was cited in the PTO-892 Notice of References Cited mailed October 18, 2023.
3 Qiao was cited in the PTO-892 Notice of References Cited mailed February 15, 2024.
4 Awwad was cited in the PTO-892 Notice of References Cited mailed March 7, 2025.
5 Ali was cited in the PTO-892 Notice of References Cited mailed October 22, 2025.
Prosecution Insights