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 .
All previously set forth rejection under 112b were overcome by amendment.
The rejection under 102 in view of Moon et al. was overcome at least by the filing of the persuasive argument supported by the declaration filed 1/2/2026.
Claim Rejections - 35 USC § 112
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 1-18 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.
The specification does not provide basis for a signal being generated by binding of an anti-ligand to a ligand.
Claim 1 has been amended to recite that the PAMmer has “a ligand serving as a label configured to generate a detectable signal” but no basis for this amendment has been provided. The specification does not teach a ligand that itself generates a detectable signal.
The claim further recites that “the anti-ligand that specifically binds to the ligand to generate the detectable signal.”
The specification teaches in paragraph 51 that a “detectable signal” refers to a signal capable of being directly sensed by the human eye or by means of a detection system.
Examples of ligands given in the specification are biotin, digoxigenin, aptamers, peptides, oligonucleotides and polysaccharides. These molecules do not “generate” a signal “upon binding.” That is, they don’t give off any signal upon binding, they simply capture or bind to their anti-ligands. The specification does not provide written description for any embodiment wherein the binding of the anti-ligand to the ligand “generates” a detectable signal, let alone the genus of them that is currently claimed.
The specification teaches a PAMmer in which a “labeled ligand indirectly generating a detectable signal” is bound to the 3’ end (¶23), but does not teach that the signal is generated by the ligand attached to the PAMmer upon binding.
The specification teaches reacting the reaction product of step (a) “with an anti-ligand that recognizes the detectable signal (¶24).” This does not teach the newly claimed anti-ligand that “binds to the ligand to generate the detectable signal.”
An “indirect” label is “capable of generating a signal only after interaction with another compound such as a substrate or binding partner (¶52).” This doesn’t teach that the binding itself generates the detectable signal, only that the binding results in the capability to generate the signal.
Claim 4 recites that the ligand is biotin and the anti-ligand is avidin or an avidin analog. When these two things bind, there is no description of a detectable signal that is released. The specification discloses an assay in which the anti-ligand is streptavidin-HRP, and the signal is generated when the HRP comes in contact with an appropriate substrate. This signal is not a result of the binding but of the enzyme modifying the substrate.
Therefore, the claims are rejected as having new matter.
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, and 4 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 is indefinite when it refers to a label configured to “generate a detectable signal only upon binding.” It is not clear what it means for the ligand (exemplified, for example as biotin) to be configured to generate a detectable signal upon binding to an anti-ligand since the exemplified ligand itself is not capable of generating a signal, and it is unclear what signal is given off “upon binding.” For example, if a fluorescently labeled anti-ligand binds to a ligand, is it the ligand giving off the signal, or the anti-ligand or the fluorophore itself? Or is something further signal directly from the ligand required by the language requiring that the ligand is configured “to generate a detectable signal”?
Claim 2 is indefinite for this same reason, as it is unclear how any of the recited ligands are configured to give off a signal “only upon binding” to anything. None of the examples themselves are known in the art “generate” signals.
Claims 15 and 16 and 18 are indefinite for the same reasons as claims 1 and 2.
Claims 11 and 12 identify the anti-ligand as having a horse radish peroxidase component, and claim 12 identifies the substrate of the HRP, so it is unclear in this embodiment, is it the ligand that generates the signal or is it the interaction between HRP and a substrate? Furthermore, although claim 12 substrates, there is actually still no step of generating a signal because there is no requirement to add the substrate to the reaction.
In claim 2, “the ligand capable of indirectly generating a detectable signal” lacks proper antecedent basis because although claim 1 recites “a ligand serving as a label” it does not mention indirectly generating a detectable signal.
In claims 3 and 4, “the anti-ligand that recognizes a detectable signal” lacks antecedent basis since although claim 1 recites an “anti-ligand” it does not mention that it “recognizes a detectable signal.”
In claim 4, “the ligand indirectly generating a detectable signal” lacks proper antecedent basis because although claim 1 recites “a ligand serving as a label” it does not mention indirectly generating a detectable signal.
Any claim not specifically enumerated is indefinite over because it depends from a rejected claim and fails to fix the indefiniteness issue.
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) 1-8, 10, and 14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Doudna et al. (US 2016/0289659) in view of Nelles et al. (2015 BioEssays, 37: 732-739. https://doi.org/10.1002/bies.201500001).
Doudna teaches reacting a dCas9/gRNA complex with a PAMmer and a biological sample isolated from a subject, wherein the dCas9/gRNA complex includes inactivated Cas9 and a guide RNA complementary to a target RNA (¶0008, ¶0011). The reference teaches that the PAMmer is an oligonucleotide can be indirectly labeled, for example by biotin (¶20, ¶0442).
The PAMmer taught by the reference includes a first 3’ hybridization region having a hybridization nucleotide sequence complementary to the target RNA, a PAM sequence, and a 5’-second hybridization region having a hybridization nucleotide sequence complementary to the target RNA (¶0008).
The reference teaches treating the reaction product of step (a) with an anti-ligand that recognizes the detectable signal (¶0110). The reference teaches that an indirect label includes biotin which can be bound by streptavin which itself can be indirectly labeled with an enzyme or directly labeled with a fluorescent protein. (¶0110, ¶0442). The reference exemplifies binding biotin to streptavidin AFTER the binding of the dCas9 complex to the RNA of interest (Figure 21D).
With regard to the claim requirement that the ligand is “configured to generate a detectable signal only upon binding to a corresponding anti-ligand” the biotin in the reference is a ligand. By itself, it does not give off a signal, it will only give off a signal when bound by it’s anti-ligand. The biotin itself never actually gives off a signal, but since biotin is a preferred embodiment for a ligand it is interpreted to meet this claim limitation.
With regard to the claim limitation, “the anti-ligand that specifically binds to the ligand to generate a detectable signal.” The reference teaches streptavidin which is a preferred anti-ligand of the instant invention and so is interpreted to meet this limitation, even though the binding of biotin to streptavidin does not in and of itself generate a detectable signal.
With regard to claims 2, 3, 4 and 10, the reference teaches an exemplary indirect labeling pair is biotin which can be bound by streptavidin which itself can be labeled (¶0110, ¶0442).
With regard to claim 5, the gRNA is a single chain guide RNA (¶0008; Figure 21D).
With regard to claims 6 and 7, the gRNA contains the same sequence as the 5’second hybridization region of the PAMmer, and the sequence is 5 to 20 nucleotides in length (¶0009, 0010; Figure 8, 21D).
With regard to claim 8, Doudna teaches that the PAM sequence is NGG (¶0012).
With regard to claim 14, Doudna teaches that the target is virus-derived RNA (¶0011).
Nelles provides an illustration of Cas9 bound to an RNA and a PAMmer. The 3’ end of the PAMmer is illustrated to be outside of the bound protein. See Figure 1B.
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It would have been obvious before the effective filing date to have labeled the 3’ end of the PAMmer taught by Doudna. Doudna does not provide instruction about where to label the PAMmer, however, Nelles illustrate that a PAMmer has a 3’end that is exposed when bound within a Cas9 complex. One would have been motivated to place the label at the 3’ end of the PAMmer in order provide a labeled molecule for a visualizing a target according to the methods taught by Doudna (442).
Claim(s) 9 and 15-17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Doudna in view of Nelles as applied to claims 1-8, 10, and 14 above, and further in view of Walter et al. (US 2019/0048415).
The teachings of Doudna in view of Nelles are given previously in this Office action and fully incorporated herein.
Doudna in teaches kits containing the elements for practicing the method (¶0012). As addressed previously, Doudna in view of Nelles teaches a method that employs the elements recited in claim 15, except, regarding claims 9 and 15, Doudna in view of Nelles does not teach a method wherein the dCas9/gRNA complex is immobilized.
Walter teaches a detection method which employs a dCas9/guide RNA complex that is immobilized on a solid substrate. See figure 3, ¶0009.
It would have been obvious to have modified the method and kit taught by Doudna in view of Nelles so as to have captured the dCas9/guide RNA complex onto a solid surface. One would have been motivated to do so in order to provide a system where the target molecules are fixed in a location for detection. A solid phase system would allow for washing away of non-complexed materials and further analysis to detect the bound species.
Claim(s) 11-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Doudna in view of Nelles as applied to claims 1-8, 10, and 14 above, and further in view of Chen et al. (Analytica Chimica Acta 880 (2015) 1–7).
Claim(s) 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Doudna in view of Nelles and Walter as applied to claim 15 above, and further in view of Chen et al. (Analytica Chimica Acta 880 (2015) 1–7)
The teachings of Doudna in view of Nelles and Doudna in view of Nelles and Walter are given previously in this Office action and fully incorporated herein.
Doudna teaches that suitable labels include an enzyme such as a peroxidase. Duodna in view of Nelles and Doudna in view of Nelles and Walter do not teach a method wherein the avidin analog is a horseradish hydrogen peroxidase conjugate of the avidin analog, a substrate as recited in claims 12 and 18, or confirming color change with “the naked eye.”
Chen teaches a colorimetric assay where a probe is labeled with biotin which is then bound with streptavidin which is conjugated via linker DNA to horseradish peroxidase which works on a tetramethylbenzidine (TMB) substrate to produce a colorimetric reaction that is visible to the “naked eye.” Figure 1, section 3.1.
It would have been obvious to have further modified the methods and kits taught by Doudna in view of Nelles and the methods and kits taught by Doudna in view of Nelles and Walter so as to have employed and provided reagents where the streptavidin is conjugated to HRP. One would have been motivated to do so in order to provide an assay whose results could be detected without the use of complex instrumentation.
Response to Remarks
Applicant argues that paragraph 442 of Doudna describes that a component of the Cas9/guide/PAMmer complex maybe detectably labeled, either directly or indirectly for visualizing the complex. Applicant argues that Doudna does not disclose a mechanism in which visualization occurs only upon a subsequent binding event between a ligand and an anti-ligand.
However, the only exemplification of a use of an indirect label (Figure 21D) in the Doudna teaches adding the anti-ligand (i.e. binding partner) after the binding of the complex to the target. Therefore, Doudna does show adding the anti-ligand after binding. Although the figure does not teach the label on the PAMmer, indirect labeling of the PAMmer is taught elsewhere in the reference. Therefore, considering the totality of the teachings of Doudna, the reference teaches indirect labeling of the PAMmer and adding the anti-ligand of the to the already bound complex.
Applicant points out that in Figure 21D the biotin tag is not at the 3’ end of the PAMmer. The rejection addresses specifically why it would have been obvious to label the 3’ end of the PAMmer, relying on Nelles to explain and support the position.
Applicant argues that when a dCas9/gRNA molecule is labeled, rather than the PAMmer as claimed detection sensitivity is lower, however, there is no evidence to support this assertion cited in the argument.
Applicant points out that claim 32 of Doudna teaches that the PAMmer is labeled with a detectably label, indirect labeling of the PAMmer is taught elsewhere in the reference.
Applicant argues that claim 32 does not “have a region that hybridizes to the target in the 3’ end direction.” First, the claim does not mention hybridizing in “the 3’ end direction,” (emphasis added) and it is not entirely clear what this argument means. Second, the argument against Doudna alone is a piecemeal analysis that does not consider the totality of the rejection.
Applicant further refers to “the PAMmer containing the fluorescent marker and quencher” binding to a target RNA. No such PAMmer is claimed, thus this argument is addressed to a feature not claimed. No claim mentions a fluorescent marker and a quencher, therefore this argument is about a feature that is not claimed.
Furthmore, with regard to the product kit claims, it is noted that all of applicant’s arguments are directed towards how the claimed products would be used and none point out any difference between the combinations of products suggested by the prior art and the claimed products.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Wang et al. (ACS Nano 2020, 14, 2497−2508) teaches a lateral flow assay that employs dCas9 in a lateral flow assay for the detection of target sequences.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/ Primary Examiner, Art Unit 1682