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 .
The examiner reviewing your application at the PTO has changed. To aid in correlating any papers for this application, all further correspondence regarding this application should be directed to examiner Sarae Bausch.
This action is in response to applicants correspondence mailed 04/06/2026. The amendment to the claims mailed 04/06/2026 has been entered.
Election/Restrictions
Applicant’s election without traverse of group I in the reply filed on 04/06/2026 is acknowledged.
Claims 1-6, 9-10, 12, 17 and 47-53 are under examination.
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, 9-10, 12, 17 and 47-53 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 recites a high Kd guide RNA specific for a signal amplification target nucleic acid molecule. The recitation of high Kd guide RNA renders the claim indefinite. It is unclear what the structural features of the guide RNA are that results in a “high Kd guide RNA”. It is unclear what is encompassed by a high Kd. Does the Kd refer to the binding association of the guide RNA to the Cas endonuclease or does the Kd refer to the binding association of the guide RNA-CRISPR complex binding to the signal amplification target nucleic acid? Additionally it is unclear what the structural features of the guide RNA encompass such that the guide RNA has a “high” Kd.
The term “high Kd” in claims 1, 3-5, 10, 12, 47, 52 and “low Kd” in claims 5-6, is a relative term which renders the claim indefinite. The term “high” and “low” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what the structural components of a high Kd and low Kd guide encompass and one of skill in the art cannot determine the metes and bounds of the claimed subject matter and would not be apprised of infringing on the claimed method.
Claim 9 recites wherein the sample is further contacted with one or more single stranded nucleic acid reporter molecules. This limitation is indefinite because it is not clear how or when this step is performed. Claim 1 requires a method of detecting a target nucleic acid molecule in a sample by contacting the sample with a Cas endonuclease, gRNA, signal amplification target nucleic acid, and a high Kd guide RNA. It is unclear when the sample is further contacted with one or more reporter molecules and how this is related to any of the active method steps of claim 1. For example, it is unclear if this step is performed after detecting a signal, if the reporter molecules are the signal that is detected and if so are these reporter molecules different from the reporter molecules generated from the CRISPR claimed method or are additional reporter molecules added to the sample and how these reporter molecules are used in the method. For example are the reporter molecules added before the contacting eh sample with the Cas complex or after and how do the reporter molecules interact with the sample. In the currently claimed method of claim 1, single stranded nucleic acid reporter molecules are generated in response to the active process steps, however these reporter molecules do not contact a sample, per se. Additionally it is unclear if the contacting a reporter molecule to the sample is further step and if so how this is distinguished from detecting a signal as recited in claim 1. It appears there is a gap between the steps of claim 1 and limitations of claim 9 and this renders the claim indefinite. One of ordinary skill in the art would not be reasonably apprised of the scope of the claims, cannot determine the metes and bounds of the claimed subject matter and would not be apprised of infringing on the claimed method.
Claims 2-6, 9-10, 47-53 depend from claim 1 and are indefinite for the reasons addressed to claim 1.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 4-6, 9-10, 17, 47-52 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Shi (2021, cited on IDS).
With regard to claim 1 and 17, Shi teaches detecting a target nucleic acid by assembling a Cas12a and gRNA for a target dsDNA (gRNA-T) (contacting sample with Cas endonuclease and gRNA specific for target nucleic acid) (preassembled) (claim 17). Shi teaches a scgRNA with self-reporting capabilities functions as a signal amplifier which outputs amplified fluorescence signals and multiple active gRNA molecules in response to Cas12a trans-cleavage activity (see fig 3a, exponential amplification, feedback loop) and (pg. 2, 1st column) (high Kd guide RNA specific for signal amplification target nucleic acid). Shi teaches the scgRNA is cleaved by a first ribonucleoprotein complex comprising Cas12a and gRNA-T (gRNA specific for target) (see fig 1). Shi teaches amplified signals are produced indicating the presence of a target nucleic acid (amplified signals, fig 1). Shi teaches after cleavage of scgRNA the resulting gRNA is used in the Cas12 complex (T2) for another input/cycle of detection (see figure 1 and fig 3a)
With regard to claim 4, Shi teaches scRNA is configured to be cleaved by the first ribonucleoprotein when the complex is activated by the target nucleic acid molecule. The scgRNA is a high Kd gRNA. High Kd gRNA has been interpreted to encompass a gRNA that binds a ribonucleoprotein complex. Because high is not defined in the claim it has been given its broadest reasonable interpretation to encompass a guide RNA that binds a ribonucleoprotein complex.
With regard to claim 5-6, Shi teaches scgRNA when cleaved by the Cas12-complex (T1) results in a gRNA therefore Shi teaches a high Kd gRNA (scgRNA) after cleavage converts into a low Kd gRNA (gRNA) (see fig 1). A bulged gRNA will have a higher Kd than a gRNA without a bulge as such Shi anticipates the claims. Shi teaches the gRNA that results from the cleavage of scgRNA binds a second ribonucleoprotein complex and is activated by the assistant probe (amplification target nucleic acid) (see T2 and assistant probe, fig 1).
With regard to claim 9, Shi teaches generating nucleic acid reporter molecules, which will be in contact with the sample in solution (see fig 1 and 3). Additionally, Shi teaches contacting the sample with scgRNA which comprises a reporter molecule.
With regard to claim 10 and 52, Shi teaches a scgRNA (high Kd gRNA) that comprises a 7 nucleotide DNA bulge (prevents formation of active RNP complex), a 20 nucleotide spacer region (homologous to target, about 20 ribonucleotide) and a 21 nucleotide handle (about 25 ribonucleotides are for Cas internalization) (combined 41 nucleotides that are “about” 45 ribonucleotides) (see fig S3 and S7).
With regard to claim 47, Shi teaches the scgRNA comprises a detectable signal moiety (See fig 1, fig 2c, 2d).
With regard to claim 48-49, Shi teaches exponentially amplified detection of DNA (see fig 1, 3a, pg. 7, 1st column last paragraph). It is noted that claim 49 does not require amplifying the nucleic acid molecule in the sample prior to contacting with the Cas endonuclease. Because claim 49 recites amplifying the target nucleic acid molecule along with the steps of claim 1, Shi anticipates the claim because Shi teaches exponential amplification of detection of DNA.
With regard to claim 50-51, She teaches the sample comprises crude DNA extractions from serum of patients (see pg. 5, 1st column, last paragraph). She teaches the sample from patients comprises partly double stranded circular DNA (rcDNA) (see pg. 5, 1st column, last paragraph).
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.
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.
Claims 12 and 53 are rejected under 35 U.S.C. 103 as being unpatentable over Shi(2021, cited on IDS) in view of Packard (US20230174977 A1).
Shi teaches detecting a target nucleic acid by assembling a Cas12a and gRNA for a target dsDNA (gRNA-T) (contacting sample with Cas endonuclease and gRNA specific for target nucleic acid) (preassembled). Shi teaches a scgRNA with self-reporting capabilities functions as a signal amplifier which outputs amplified fluorescence signals and multiple active gRNA molecules in response to Cas12a trans-cleavage activity (see fig 3a, exponential amplification, feedback loop) (pg. 2, 1st column) (high Kd guide RNA specific for signal amplification target nucleic acid). Shi teaches the scgRNA is cleaved by a first ribonucleoprotein complex comprising Cas12a and gRNA-T (gRNA specific for target) (see fig 1). Shi teaches amplified signals are produced indicating the presence of a target nucleic acid (amplified signals, fig 1). Shi teaches after cleavage of scgRNA the resulting gRNA is used in the Cas12 complex (T2) for another input/cycle of detection (see figure 1 and fig 3a). Shi teaches the scgRNA comprises bulge but is not circular or modified with internucleoside linkages.
However modification to guide RNA was known in the art. Packard teaches engineering guide RNAs. Packard teaches a circular guide RNA can be formed by forming a covalent linkage at the 5’ and 3’ end (see para 124-125). Packard teaches the linkage can include azide based linkage (modified linkage provide nuclease resistance). Packard teaches circular guide RNA can comprise a first spacer domain, targeting domain, a second domain (see para 130). The covalent linkage will encompass a portion that prevents formation of an active RNP complex and comprise 2 nucleotides. Packard teaches the circular engineered polynucleotide can prevent degradation, increase half-life in vitro, increase stability and prevent hydrolytic degradation (see para 95 and 97)
Therefore, it would have been prima facie obvious to one of ordinary skill in the art to modify the scgRNA of Shi to include a circularized scgRNA with a modified internucleoside linkage as taught by Packard to allow for a more stabile guide RNA. The ordinary artisan would have been motived to modify the scgRNA of Shi and link the guide RNA to produce a circularized scgRNA to prevent degradation, increase half life and prevent hydrolytic degradation because Packard teaches modifying guide RNA into circularized guide RNA to prevent degradation, increase half-life and prevent hydrolytic degradation. The ordinary artisan would have had a reasonable expectation of success to link the 5’ and 3’ of the scgRNA taught by Shi to produce and use a circular guide RNA because Packard teaches the benefits of circularized guide RNA including increased half-life in vitro and Shi teaches an assay that is a feedback circuit assay thus a circularized scgRNA would be beneficial in the method of Shi to allow for less degradation and more stability, as taught by Packard.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SARAE L BAUSCH whose telephone number is (571)272-2912. The examiner can normally be reached M-F 9a-4p.
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/SARAE L BAUSCH/Primary Examiner, Art Unit 1699
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