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 .
Claim Status
Claims 1-14 are pending.
Information Disclosure Statement
The information disclosure statements (IDS) filed 22 June 2023, 23 September 2024, 27 October 2025, and 31 October 2025 are considered, initialed, and attached hereto. Non-patent Literature Document 6 (R. Watanabe et al., “Rapid Digital Detection Technology for Novel Coronavirus”) in the IDS filed 22 June 2023 was not considered because the document was not in English and a concise explanation of the relevance or translation was not provided. Foreign Patent Document 5 (WO 2019/098301) in the IDS filed 27 October 2025 was not considered because the document was not in English and a concise explanation of the relevance or translation was not provided.
Specification
The use of the terms Iowa Black, IDT, 3M, Fomblin, Solvay, Sigma-Aldrich, MBPTrap, GE Healthcare, HiTrap, Superdex, CYTOP, AGC, Samco, KAYAKU, Union, Alexa, Triton X-100, Diamond Princess, Dynabeads, and MyOne, which are trade names or a marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 1 is objected to because claim 1 lines 12-15 recite “thereby forming the three-part complex in a case where the target nucleic acid fragment is present in the sample, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher” on the same line immediately following the recitation “the contact is performed in a reaction space having a volume of 10 aL to 100 pL”. The “thereby…” clause appears to be stating a condition that may arise when step (a) has been performed, which is how it will be interpreted for the purpose of examination, but the placement in line with the reaction space limitation suggests that it is specific to the reaction space limitation. Placement of the “thereby…” clause on a new line would obviate this objection.
Claim 2 is objected to because claim 2 lines 11-13 recite “thereby forming the three-part complex in the presence of the target nucleic acid fragment in the well, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher” on the same line immediately following the recitation “(a2) sealing each well of the array with a sealing liquid”. The “thereby…” clause appears to be stating a condition that may arise when step (a) has been performed, which is how it will be interpreted for the purpose of examination, but the placement in line with the sealing step suggests that it is specific to and caused by the sealing step. Placement of the “thereby…” clause on a new line would obviate this objection.
Claim 3 is objected to because claim 2 lines 14-18 recite “thereby dehydrating a content of the wells, reducing a volume, causing accumulation of the content inside the second well, forming the three-part complex in the presence of the target nucleic acid fragment in the well, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher” on the same line immediately following the recitation “(a3’) replacing the sealing liquid with a water-absorbing organic solvent”. The clause “forming the three-part complex in the presence of the target nucleic acid fragment in the well, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher” appears to be stating a condition that may arise when step (a) has been performed, which is how it will be interpreted for the purpose of examination, but the placement in line with the replacement step suggests that it is specific to and caused by the step of replacing the sealing liquid with a water-absorbing organic solvent. Placement of either the entire “thereby…” clause or the portion “thereby forming…” on a new line would obviate this objection.
Claims 1 and 10 are objected to because claim 1 lines 9-10 and claim 10 lines 9-10 recite “in a case where the fluorescent substance cleaved by the nuclease activity of the three-part complex is separated from the quencher”. The plain meaning of this phrase would suggest that a case occurs wherein nuclease activity of the complex cleaves a fluorescent substance that is labeling the substrate nucleic acid. However, one of ordinary skill in the art would understand the effect of nuclease activity is the cleavage of a nucleic acid, not cleavage of fluorescent substances such as the fluorophores FAM and HEX that are provided as examples in the instant specification ([0073]). Because the drawings (Fig. 1B) and specification (“substrate nucleic acid fragments 150 that are present around the tripartite complex 100’ are cleaved”, [0019]; “a Cas12 protein leaves a single-stranded DNA as a substrate” and “a Cas13 protein cleaves a single-stranded RNA as a substrate”, [0042]) indicate that the nuclease activity cleaves nucleic acids and does not provide any suggestion that the nuclease activity can cleave a fluorophore outside of recitations of identical language to the phrase in the claim that is objected to, for the purpose of examination this phrase is interpreted in view of the specification as referring to a case where the fluorescent substance is separated from the quencher due to a cleavage caused by nuclease activity of the three-part complex.
Appropriate correction is required.
Claim Interpretation
Claim 1 lines 9-11 recite the conditional limitation “in a case where the fluorescent substance cleaved by the nuclease activity of the three-part complex is separate from the quencher, fluorescent light is emitted by irradiation with excitation light”. It is noted that the broadest reasonable interpretation of a method requires only those steps that must be performed and does not include steps that are not required (see MPEP §2111.04 II.). Given that the recitation “in a case where” is clearly conditional in nature and the recited “target nucleic acid fragment” is not required to be present for the method to be done, this claim language is not given patentable weight when comparing the claim 1 and the claims that depend from it with the prior art. This same rationale applies to the recitation in claim 1 lines 12-15 of “thereby forming the three-part complex in a case where the target nucleic acid fragment is present in the sample, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher”, as the use of the phrase “in a case where” and lack of requirement for the presence of the target nucleic acid fragment renders this claim limitation conditional such that it is not given patentable weight.
Claim 2 lines 11-13 recite the conditional limitation “thereby forming the three-part complex in the presence of the target nucleic acid fragment in the well, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher”. The same rationale as in the above paragraph applies, as the use of “in the presence of” creates a condition for the forming, cleaving, and separating limitation and along with the lack of requirement for the presence of the target nucleic acid fragment renders the claim limitation conditional such that it is not given patentable weight.
Claim 3 lines 16-18 recite the conditional limitation “forming the three-part complex in the presence of the target nucleic acid fragment in the content, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher”. The same rationale as in the above paragraph applies, as the use of “in the presence of” creates a condition for the forming, cleaving, and separating limitation and along with the lack of requirement for the presence of the target nucleic acid fragment renders the claim limitation conditional such that it is not given patentable weight.
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.
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.
Claims 1-2, 6-11, and 13-14 are rejected under 35 U.S.C. 103 as being unpatentable over Ching et al. (US PG PUB 2024/0294970, 102(a)(2) effectively filed date of 17 December 2020), herein Ching, in view of Makino and Kunitomi (EP 3101115, published 7 December 2016, cited in IDS), herein Makino.
Regarding claim 1, Ching teaches a method for detecting a target nucleic acid fragment in a sample (“a method of assaying for a plurality of different target nucleic acids in a sample” [0013]) comprising contacting the sample (“contacting a surface with the sample” [0013]) with a gRNA complementary to the target nucleic acid fragment (“wherein the surface comprises: (i) […] non-naturally occurring guide nucleic acids” [0013]; “the guide nucleic acid is complementary to the target nucleic acid” [0199]), a CRISPR/Cas family protein wherein the CRISPR/Cas family protein expresses nuclease activity after forming a three-part complex with the gRNA and the target nucleic acid fragment (“forming activated complexes […], wherein the activated complexes comprise (i) one of the […] guide nucleic acids, (ii) a programmable nuclease, and (iii) one of the different target nucleic acids” [0013]; “Several programmable nucleases are consistent with the systems and methods of the present disclosure. For example, CRISPR/Cas enzymes are programmable nucleases that can be used to implement the methods and systems disclosed herein” [0083]) and the CRISPR/Cas family protein is immobilized on a solid phase (“in some embodiments, the programmable nuclease is immobilized to the device surface” [0197], Fig. 1A-B), and a substrate nucleic acid fragment (“the surface comprises […] (ii) a plurality of reporters” [0013]) wherein the substrate nucleic acid fragment is labeled with a fluorescent substance and a quencher (“the reporter may comprise a fluorescent label joined to a quencher by a short polynucleotide sequence” [0081]). Ching also teaches that in a case where the target nucleic acid fragment is present the three-part complex is formed (“the trans cleavage activity of the CRISPR enzyme can be activated when the guide nucleic acid comprising a tracrRNA and crRNA are complexed with the target nucleic acid” [0087]), the substrate nucleic acid is cleaved by nuclease activity (a programmable nuclease as disclosed herein can, in some cases, bind to a target sequence or target nucleic acid to initiate trans cleavage of a reporter molecule” [0081]), and the fluorescent substance is separated from the quencher (“upon cleavage of the polynucleotide, the fluorescent label is separated from the quencher” [0081]). Ching also teaches that this separation of the fluorescent label from the quencher leads to a detectable indication of the presence of the target nucleic acid fragment based on fluorescent light emitted by the fluorescent substance in response to irradiation with excitation light (“cleavage of the polynucleotide results in a change in a signal […] little to no fluorescence is detectable from the fluorescent label when joined to the quencher. However, upon cleavage of the polynucleotide, the fluorescent label is separated from the quencher, resulting in a significant and detectable increase in fluorescent signal upon excitation of the label” [0081]).
However, Ching does not teach the contacting step being performed in a reaction space having a volume of 10 aL to 100 pL. This deficiency is made up for in the teachings of Makino.
Regarding claim 1, Makino teaches a “biomolecule analysis method” ([0018]) applicable to detection of target nucleic acids (“as a biomolecule to be analyzed, any of DNA, RNA, miRNA, mRNA […], and a protein is selected” [0042]) by fluorescence (“may generate a signal by any one of fluorescence” [0028]; “detects […] fluorescence […] as a signal” [0082]. Makino teaches that this method is performed so that the reaction occurs in microspaces (“as a result, each of the microspaces 11 becomes an independent reaction chamber”) that have a volume that is exemplified as being less than or equal to 100 pL (“for example, the volume of the microspace 11 is equal to or less than 100 picoliters” [0048]). Makino also teaches that the same biomolecules can be analyze using a second embodiment ([0074-0075]), wherein the reaction space (“the amount of liquid that fills the wells 26 may be appropriately set according to the number of through holes 25a” [0119]; “the plurality of well 26 becomes a plurality of independent reaction chambers 36 (reaction containers for nucleic acid detection) [0120]; FIGs 6-8) may have a volume of about 60 fL (“the volume of the through hole 25a is about 60 femtoliters” [0079]). Because the 60 fL embodiment falls within the claimed range of 10aL to 100 pL, the claimed range is anticipated (MPEP §2131.03 I.). Additionally, the claimed range, a reaction space having a volume of 10 aL to 100 pL, overlaps with the disclosed reaction space volumes of less than or equal to 100pL, so a prima facie case of obviousness exists (MPEP §2144.05 I.).
Regarding claim 2, Makino teaches that the method of detection wherein the contacting of reagents occurs in each well of a well array and the reaction space is a space inside each well (“the array device 20 in which each of the wells 26 is filled with the invader reaction reagent and DNA is incubated” [0121]). Ching teaches the CRISPR/Cas family protein being immobilized on an inner surface of a well (“the programmable nuclease probe (e.g., a CRISPR probe) can be immobilized to an immobilization matrix. In some cases, the interior side of the immobilization matrix may be exposed to an inside wall” [0194]; see Example 4 in its entirety, particularly: “96-well streptavidin coated plate” [0353] and “results of this experiment (See FIGS. 10A-10F) […] FIGS. 10A and 10D show results where […] a complex of biotinylated RNA and CAS protein were immobilized” [0368]). Makino teaches sealing each well of the well array with a sealing liquid after the components of the reaction are added (“the oil sealing solution 22 seals the liquid in the plurality of wells 26, and as a result, the plurality of well 26 becomes a plurality of independent reaction chambers 36” [0120]). Regarding the limitation: “(a1) introducing the sample and the substrate nucleic acid fragment into each well of the well array in a case where the CRISPR/Cas family protein has formed a two-part complex with the gRNA in advance, and introducing the sample, the gRNA, and the substrate nucleic acid fragment into each well of the well array in a case where the CRISPR/Cas family protein has not formed the two-part complex with the gRNA in advance”, this limitation claims two alternative orders of combining the components of the reaction, either first adding the gRNA before the sample and substrate such that the gRNA complexes with the CRISPR/Cas family protein or adding the gRNA with the sample and substrate. Since Ching teaches combining all of these components (see discussion of claim 1 above) and the “selection of any order of mixing ingredients is prima facie obvious” (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); MPEP §2144.04 IV. C.), these orders of combining the components of the reaction are obvious. The conditional limitation “thereby […] quencher” in lines 11-13 of claim 2 is equivalent to the conditional limitation “thereby […] quencher” in lines 12-15 of claim 1, so it is taught by Ching as described for claim 1 above.
Regarding claim 6, Ching teaches a method wherein the CRISPR/Cas family protein is immobilized on a surface of a particle (e.g. a bead) (“a surface at a known location” [0006]; “programmable nucleases immobilized at the known locations” [0009]; and “the surface can comprise a surface of a fluidic chamber or a bead” [0010]). Ching also teaches a method wherein the sample, the gRNA, and the CRISPR/Cas family protein are mixed in a container (e.g. detection chamber) (“The method can comprise receiving the plurality of sub-samples in a detection chamber and contacting the plurality of sub-samples with at least one programmable nuclease probe disposed on a surface of said detection chamber. The at least one programmable nuclease probe can comprise a guide nucleic acid complexed with a programmable nuclease” [0265]) and form the three-part complex including the CRISPR/Cas family protein, the gRNA, and the target nucleic acid fragment on the particle (“forming activated complexes at one or more of the known locations, wherein the activated complexes comprise (i) one of the different non-naturally occurring guide nucleic acids, (ii) a programmable nuclease, and (iii) one of the different target nucleic acids” [0013] and the known locations are on a surface that can comprise a bead as described above).
Regarding claim 7, Ching teaches a method wherein the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein (“In some embodiments, the type V CRISPR/Cas effector protein is a Cas12 protein” [0018]; “In some embodiments, the type VI CRISPR/Cas effector protein is a Cas13 protein” [0018]).
Regarding claim 8, Makino teaches that for a reaction performed in the disclosed microspace (discussed with regard to claim 1 above), 0 or 1 of the target nucleic acid fragment is introduced into the reaction space (“if the invader reaction is performed in a microspace, the number of molecules as a target of analysis contained in a single well can become equal to or less than 1” [0013]; “the volume of the microspace 11 is set based on a liquid amount in which the number of biomolecules as target of analysis becomes equal to or less than 1 per well” [0049]; “the volume of each well 26 is set based on a liquid amount in which the number of biomolecules as target of analysis becomes equal to or less than 1 per well” [0087]).
Regarding claim 9, Ching teaches a method wherein the sample is a biological sample ([0146]) and step (a) is performed without purifying the target nucleic acid fragment from the biological sample (“In some cases, the one or more sample preparation steps can comprise physical filtration of non-target materials using a macro filter, nucleic acid purification, lysis, heat inactivation, or adding one or more enzymes or reagents to prepare the sample for target detection” emphasis added [0165]).
Regarding claim 10, Makino teaches a kit for detecting a target nucleic acid fragment comprising a substrate having a surface (“a biomolecule analysis kit according to a first aspect of the present invention includes a reaction container configured to perform an enzymatic reaction” [0019]; also see [0024, 0035]) on which a well having a volume of 10 aL to 100 pL is formed (see discussion of claim 1 above). Ching teaches one such enzymatic reaction comprising a gRNA complementary to the target nucleic acid fragment; a CRISPR/Cas family protein immobilized on a solid phase; and a substrate nucleic acid fragment, wherein the CRISPR/Cas family protein expresses nuclease activity after forming a three-part complex with the gRNA and the target nucleic acid fragment, the substate nucleic acid fragment is labeled with a fluorescent substance and a quencher, and in a case where the nuclease activity of the three-part complex separates the fluorescent substance from the quencher, fluorescent light is emitted by irradiation with excitation light as discussed for claim 1 above.
Regarding claim 11, Ching teaches the CRISPR/Cas family protein being immobilized on an inner surface of a well as discussed for claim 2 above.
Regarding claim 13, Ching teaches the CRISPR/Cas family protein being immobilized on a surface of a particle as discussed for claim 6 above.
Regarding claim 14, Ching teaches the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein as discussed for claim 7 above.
In view of the teachings of Makino, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the methods of Ching so as to have reduced the quantities and volumes taught by Makino and to employ the methods of Ching in kits utilizing reduced quantities and volumes taught by Makino. One of ordinary skill in the art would have been motivated to have made such a modification for advantages as taught by Makino of the use of such smaller volumes, such as the teaching that smaller reaction spaces facilitate shorter reaction times (Makino [0048, 0080]). One of ordinary skill in the art would have a reasonable expectation of success in combining the teachings of Ching and Makino because both teach methods and structures for performing enzymatic detection of nucleic acids that are detected by fluorescence. Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Ching et al. (US PG PUB 2024/0294970, 102(a)(2) effectively filed date of 17 December 2020), herein Ching, in view of Makino and Kunitomi (EP 3101115, published 7 December 2016, cited in IDS), herein Makino, as applied to claims 1-2, 6-11, and 13-14 above, and further in view of Simon et al. (US PG PUB 2014/0004539, published 2 January 2014 with effectively filed date 15 June 2012), herein Simon.
Regarding claim 12, Ching and Makino teach a kit for detecting a target nucleic acid fragment according to claim 11 as discussed for claim 11 above. However, Ching and Makino do not teach a well having a first well and a second well arranged at a bottom of the first well and having a smaller capacity than the first well, and the CRISPR/Cas family protein being immobilized on an inner surface of the second well. This deficiency is made up for in the teachings of Simon.
Regarding claim 12, Simon teaches a well that has a first well (Figure 1(A) “Large Sample Well”) and a second well arranged at a bottom of the first well and having a smaller capacity than the first well (Figure 1(A) “Smaller Wells”; “FIG. 1 […] (a) A side view of the plate shows that each of the 96 large wells contains 4 smaller wells” [0010]), effectively creating a separate reaction space in each second smaller well (“acceptor beads and biotinylated detection antibodies against 4 different antigens […] were dispensed into each of the four DEX wells per larger PEG well” [0110]). Because Ching teaches the CRISPR/Cas family protein being immobilized on an inner surface of a well that makes up the reaction space (see discussion of claim 2 above) and the reaction space of Simon is the second smaller well, the combination of Ching, Makino, and Simon teach that the CRISPR/Cas family protein is immobilized on an inner surface of the second well. Additionally, Ching teaches that their method can by multiplexed by “spatial multiplexing wherein multiple different target nucleic acids are detected at the same time, but the reactions are spatially separated” ([0238]) and Simon teaches that having smaller wells inside the larger wells allows for spatial multiplexing by allowing “for the simultaneous detection of four antigens (4-plex assays)” ([0010]).
In view of the teachings of Simon and Ching, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the spatial multiplexing described in Ching in view Makino with the spatial multiplexing using the wells taught by Simon. One of ordinary skill in the art would recognize that both provide the function of spatial multiplexing. One of ordinary skill in the art would find that the results of the substitution would have been predictable since both methods of multiplexing spatially separate individual reactions. Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claims 3-5 are rejected under 35 U.S.C. 103 as being unpatentable over Ching et al. (US PG PUB 2024/0294970, 102(a)(2) effectively filed date of 17 December 2020), herein Ching, in view of Makino and Kunitomi (EP 3101115, published 7 December 2016, cited in IDS), herein Makino, and in view of Simon et al. (US PG PUB 2014/0004539, published 2 January 2014 with effectively filed date 15 June 2012), herein Simon as applied to claim 12 above, and further in view of Aygan ("Nucleic Acid Extraction from Clinical Specimens for PCR Applications", Turk J Biol 30, 107-120 (2006)).
Regarding claim 3, Ching and Makino teach, as discussed for claims 1 and 2 above, a method according to claim 1 wherein step (a) is performed in each well of a well array and step (a) includes the steps of (a1’) introducing the sample and the substrate nucleic acid fragment into each well of the well array in a case where the CRISPR/Cas family protein has formed a two-part complex with the gRNA in advance, and introducing the sample, the gRNA, and the substrate nucleic acid fragment into each well of the well array in a case where the CRISPR/Cas family protein has not formed the two-part complex with the gRNA in advance, and (a2’) sealing each well of the well array with a sealing liquid, thereby forming the three-part complex in the presence of the target nucleic acid fragment in the content, cleaving the substrate nucleic acid fragment, and separating the fluorescent substance from the quencher. However, Ching and Makino do not teach a method wherein each well has a first well and a second well arranged at a bottom of the first well and having a smaller capacity than the first well, the reaction space is a space inside the second well, and the CRISPR/Cas family protein is immobilized on an inner surface of the second well. This deficiency is made up for in the teachings of Simon.
Regarding claim 3, Simon teaches, as discussed for claim 12 above, methods using a well that has a first well and a second well arranged at a bottom of the first well and having a smaller capacity than the first well that effectively creates a separate reaction space in each second smaller well. As discussed for claim 12 above, the combination of Ching, Makino, and Simon teach that the CRISPR/Cas family protein is immobilized on an inner surface of the second well. However, the combination of Ching, Makino, and Simon do not teach replacing the sealing liquid with a water-absorbing organic solvent, thereby dehydrating the content of the wells, reducing a volume, causing accumulation of the content inside the second well. This deficiency is made up for in the teachings of Aygan.
Regarding claim 3, Aygan teaches a method of concentrating DNA molecules wherein the sample is contacted with a water-absorbing organic solvent (“2-butanol is mixed vigorously with the sample” page 7 column 2 paragraph 5), which is the same effect that replacing the sealing liquid with a water-absorbing organic solvent will have. Aygan teaches that this dehydrates the sample, reducing a volume, causing accumulation of the content (“the volume of the aqueous, DNA-containing lower phase will be reduced as water partitions into the butanol phase, thus increasing the DNA concentration”, page 7 column 2 paragraph 5).
Regarding claim 4, Makino teaches that the sealing liquid is a fluorine-based liquid or mineral oil (“as the oil sealing solution 22, mineral oil, FC40 as a fluorine-based liquid, or the like can be used” [0106]).
Regarding claim 5, Aygan teaches that the water-absorbing organic solvent is a linear saturated aliphatic alcohol having 4 carbon atoms (“2-butanol” page 7 column 2 paragraph 5).
In view of the teachings of Simon and Ching, as discussed for claim 12 above, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the spatial multiplexing described by Ching in view Makino with the spatial multiplexing using the wells taught by Simon. One of ordinary skill in the art would recognize that both provide the function of spatial multiplexing. One of ordinary skill in the art would find that the results of the substitution would have been predictable since both methods of multiplexing spatially separate individual reactions. Therefore, the combination of Ching, Makino, and Simon would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Makino teaches that “a method of shortening the time it takes for the signal concentration to become saturated” is advantageous over methods that are slower, which would motivate one of ordinary skill in the art to combine the teachings of Ching, Makino, and Simon with methods of increasing the concentration of a nucleic acid signal (Makino [0012]). In view of this teaching of Makino and Aygan’s teaching of using butanol as a standard method of increasing the concentration of a nucleic acid, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine Aygan’s method of using butanol to increase DNA concentration with the method for detecting a target nucleic acid taught by the combination of Ching, Makino, and Simon. One of ordinary skill in the art would have a reasonable expectation of success in combining the teachings of Aygan with the teachings of Ching, Makino, and Simon because Aygan teaches a standard method pertaining to manipulation of a nucleic acid in solution and the Ching teaches a method of manipulating nucleic acids in solution in order to detect the presence of a target nucleic acid. Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
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 1-2, 7-8, 10-11 and 14 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 2-3 and 5 of U.S. Patent No. 12,522,859. Although the claims at issue are not identical, they are not patentably distinct from each other because the '859 claims anticipate or make obvious the instant claims.
Regarding instant claim 1, claim 3 of ‘859 depends on claim 1, which together recite a method for detecting a target nucleic acid fragment in a sample comprising steps with language identical or equivalent to the language of instant claim 1. Via its dependency on claim 1, claim 3 of ‘859 differs from the instant claim 1 in that it requires that the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein, the reaction space is a well formed in a baseplate, the opening of the well is sealed by a lipid membrane, and the method is performed without amplifying the target nucleic acid fragment. However, nothing in the language of the instant claims exclude embodiments in which these requirements take place, and in fact instant claim 2 requires that the components are contacted in a well and that the well is sealed with a sealing liquid, which a lipid membrane is a species of and instant claim 7 requires that the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein.
Regarding instant claim 2, claim 3 of ‘859 recites identical or equivalent language to instant claim 2 as discussed for instant claim 1 above, with the exception of the limitation: “(a1) introducing the sample and the substrate nucleic acid fragment into each well of the well array in a case where the CRISPR/Cas family protein has formed a two-part complex with the gRNA in advance, and introducing the sample, the gRNA, and the substrate nucleic acid fragment into each well of the well array in a case where the CRISPR/Cas family protein has not formed the two-part complex with the gRNA in advance”. As discussed in the 35 U.S.C. 103 rejection of claim 2 above, this limitation claims two alternative orders of combining the components of the reaction, either first adding the gRNA before the sample and substrate such that the gRNA complexes with the CRISPR/Cas family protein or adding the gRNA with the sample and substrate. Since ‘859 recites combining all of these components and the “selection of any order of mixing ingredients is prima facie obvious” (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); MPEP §2144.04 IV. C.), these orders of combining the components of the reaction are obvious. Claim 3 of ‘859 via its dependency on claim 1 recites sealing each well of the well array with a sealing liquid since a lipid membrane is an embodiment of a sealing liquid.
Regarding instant claim 7, claim 3 of ‘859 via its dependency on claim 1 recites that the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein.
Regarding instant claim 8, claim 2 of ‘859 recites a variation of the method of claim 1 wherein 0 or 1 molecule of the target nucleic acid fragment is introduced into the reaction space. Though claim 2 of ‘859 does not recite that the CRISPR/Cas family protein is immobilized, claim 3 of ‘859 recites that the CRISPR/Cas family protein is immobilized and it would be obvious to combine claims 2 and 3 of ‘859 to obtain instant claim 8 because both depend on claim 1 of ‘859.
Regarding instant claim 10, claim 5 of ‘859 depends on claim 4, which together recite a kit for detecting a target nucleic acid fragment in a sample comprising components with language identical or equivalent to the language of instant claim 10. Via its dependency on claim 4, claim 5 of ‘859 differs from instant claim 10 in that it requires that the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein and that the opening of the well is sealed by a lipid membrane. However, nothing in the language of the instant claims exclude embodiments in which these requirements take place, and in fact instant claim 14 requires that the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein.
Regarding instant claim 11, claim 5 of ‘859 recites that the CRISPR/Cas family protein is immobilized on an inner surface of the well.
Regarding instant claim 14, claim 5 of ‘859 via its dependency on claim 4 recites that the CRISPR/Cas family protein is a Cas12 protein or a Cas13 protein.
Claims 1, 6, 9-10, and 13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3 and 5 of U.S. Patent No. 12,522,859 and further in view of Ching et al. (US PG PUB 2024/0294970, 102(a)(2) effectively filed date of 17 December 2020), herein Ching.
Regarding instant claim 1, claim 3 of ‘859 teaches the method of instant claim 1 as discussed in the rejection of instant claim 1 on the ground of nonstatutory double patenting as being unpatentable over ‘859.
Regarding instant claim 6, claim 3 of ‘859 recites a method according to instant claim 1 as described for instant claim 1 above. However, ‘859 does not claim a method wherein the CRISPR/Cas family protein is immobilized on a surface of a particle. This deficiency is made up for in the teachings of Ching.
Regarding instant claim 6, Ching teaches a method wherein the CRISPR/Cas family protein is immobilized on a surface of a particle (e.g. a bead) (“a surface at a known location” [0006]; “programmable nucleases immobilized at the known locations” [0009]; and “the surface can comprise a surface of a fluidic chamber or a bead” [0010]). Ching also teaches a method wherein the sample, the gRNA, and the CRISPR/Cas family protein are mixed in a container (e.g. detection chamber) (“The method can comprise receiving the plurality of sub-samples in a detection chamber and contacting the plurality of sub-samples with at least one programmable nuclease probe disposed on a surface of said detection chamber. The at least one programmable nuclease probe can comprise a guide nucleic acid complexed with a programmable nuclease” [0265]) and form the three-part complex including the CRISPR/Cas family protein, the gRNA, and the target nucleic acid fragment on the particle (“forming activated complexes at one or more of the known locations, wherein the activated complexes comprise (i) one of the different non-naturally occurring guide nucleic acids, (ii) a programmable nuclease, and (iii) one of the different target nucleic acids” [0013] and the known locations are on a surface that can comprise a bead as described above).
Regarding instant claim 9, Ching teaches a method wherein the sample is a biological sample ([0146]) and step (a) is performed without purifying the target nucleic acid fragment from the biological sample (“In some cases, the one or more sample preparation steps can comprise physical filtration of non-target materials using a macro filter, nucleic acid purification, lysis, heat inactivation, or adding one or more enzymes or reagents to prepare the sample for target detection” emphasis added [0165]).
Regarding instant claim 10, claim 5 of ‘859 teaches the kit of instant claim 10 as discussed in the rejection of instant claim 10 on the ground of nonstatutory double patenting as being unpatentable over ‘859.
Regarding instant claim 13, claim 5 of ‘859 recites a kit according to instant claim 10 as described for instant claim 10 above. However, ‘859 does not claim a kit wherein the CRISPR/Cas family protein is immobilized on a surface of a particle. This deficiency is made up for in the teachings of Ching.
Regarding instant claim 13, Ching teaches the CRISPR/Cas family protein being immobilized on a surface of a particle as discussed for instant claim 6 above.
In view of the teachings of ‘859 and Ching, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the methods of ‘859 with the methods of Ching so as to immobilize the CRISPR/Cas family protein to the surface of a particle and to perform the method without purifying the target nucleic acid fragment from the biological sample. Both ‘859 and Ching are in the same field of endeavor, using CRISPR/Cas family proteins to detect target nucleic acids, and the combined elements of the method of Ching would merely perform the same function in the combination of ‘859 and Ching as they do in Ching alone. Due to being in the same field of endeavor and the elements of Ching performing the same function they are disclosed as performing, one of ordinary skill in the art would recognize that the results of the combination of ‘859 and Ching are predictable. Therefore, instant claims 6, 9, and 13 are obvious variations of claims 3 and 5 in ‘859 in view of Ching.
Claims 10-12 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 5 of U.S. Patent No. 12,522,859 and further in view of Simon et al. (US PG PUB 2014/0004539, published 2 January 2014 with effectively filed date 15 June 2012), herein Simon.
Regarding instant claim 10, claim 5 of ‘859 teaches the kit of instant claim 10 as discussed in the rejection of instant claim 10 on the ground of nonstatutory double patenting as being unpatentable over ‘859.
Regarding instant claim 11, claim 5 of ‘859 teaches the kit of instant claim 11 as discussed in the rejection of instant claim 11 on the ground of nonstatutory double patenting as being unpatentable over ‘859.
Regarding instant claim 12, claim 5 of ‘859 recites a kit according to instant claim 11 as described for instant claim 11 above. However, ‘859 does not claim a kit wherein the well has a first well and a second well arranged at a bottom of the first well and having a smaller capacity than the first well, and the CRISPR/Cas family protein is immobilized on the inner surface of the second well. This deficiency is made up for in the teachings of Simon.
Regarding instant claim 12, Simon teaches a well that has a first well (Figure 1(A) “Large Sample Well”) and a second well arranged at a bottom of the first well and having a smaller capacity than the first well (Figure 1(A) “Smaller Wells”; “FIG. 1 […] (a) A side view of the plate shows that each of the 96 large wells contains 4 smaller wells” [0010]), effectively creating a separate reaction space in each second smaller well (“acceptor beads and biotinylated detection antibodies against 4 different antigens […] were dispensed into each of the four DEX wells per larger PEG well” [0110]). Because claim 5 of ‘859 recites the CRISPR/Cas family protein being immobilized on an inner surface of a well where the reaction occurs and the reaction space of Simon is the second smaller well, the combination of ‘859 and Simon is a kit wherein the CRISPR/Cas family protein is immobilized on an inner surface of the second well. Additionally, Simon teaches that having smaller wells inside the larger wells is advantageous because it allows for spatial multiplexing by allowing “for the simultaneous detection of four antigens (4-plex assays)” ([0010]).
In view of Simon’s teaching that their system of having a first well and a second well arranged at a bottom of the first well has the advantage in that it allows for spatial multiplexing, one of ordinary skill in the art would be motivated to combine Simon with the kit of ‘859. One of ordinary skill in the art would have a reasonable expectation of success because both Simon and ‘859 are reciting kits in which the reaction space is the interior of a well. Therefore, instant claim 12 is an obvious variation of claim 5 of ‘859 in view of Simon.
Claims 1 and 3-5 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 3 of U.S. Patent No. 12,522,859 in view of Ching et al. (US PG PUB 2024/0294970, 102(a)(2) effectively filed date of 17 December 2020), herein Ching, Makino and Kunitomi (EP 3101115, published 7 December 2016, cited in IDS), herein Makino, Simon et al. (US PG PUB 2014/0004539, published 2 January 2014 with effectively filed date 15 June 2012), herein Simon, and Aygan ("Nucleic Acid Extraction from Clinical Specimens for PCR Applications", Turk J Biol 30, 107-120 (2006)).
Regarding instant claim 1, claim 3 of ‘859 teaches the method of instant claim 1 as discussed in the rejection of instant claim 1 on the ground of nonstatutory double patenting as being unpatentable over ‘859.
Regarding instant claim 3, claim 3 of ‘859 teaches (a1’) as discussed for (a1) of instant claim 2 in the rejection of instant claim 2 on the ground of nonstatutory double patenting as being unpatentable over ‘859 above since (a1’) and (a1) are identical language, and via its dependency on claim 1 recites sealing each well of the well array with a sealing liquid since a lipid membrane is an embodiment of a sealing liquid. However, claim 3 of ‘859 does not teach that each well has a first well and a second well arranged at a bottom of the first well and having a smaller capacity than the first well, the reaction space is a space inside of the second well, that the CRISPR/Cas family protein is immobilized on an inner surface of the second well and replacing the sealing liquid with a water-absorbing organic solvent. These deficiencies are made up for in the teaching of Simon and the teaching of Aygan, which are obvious to combine with ‘859 in view of Ching and Makino.
Regarding instant claim 3, as discussed in the 35 U.S.C. 103 rejection of claim 3 above, Simon and Aygan teach that each well has a first well and a second well arranged at a bottom of the first well and having a smaller capacity than the first well, the reaction space is a space inside of the second well, that the CRISPR/Cas family protein is immobilized on an inner surface of the second well and replacing the sealing liquid with a water-absorbing organic solvent.
Regarding instant claim 4, as discussed in the 35 U.S.C. 103 rejection of claim 4 above, Makino teaches that a sealing liquid that is a fluorine-based liquid or mineral oil.
Regarding instant claim 5, as discussed in the 35 U.S.C. 103 rejection of claim 5 above, Aygan teaches that a water-absorbing organic solvent is a linear saturated aliphatic alcohol having 4 carbon atoms.
It would be obvious to combine the teachings of Simon with ‘859 for the reasons discussed in the rejection of claims 10-12 as being unpatentable over ‘859 in view of Simon above. It would be obvious to combine the teachings of Ching with Simon and ‘859 for the same reason it is obvious to combine Ching and ‘859 as discussed in the rejection of claims 1, 6, 9-10, and 13 as being unpatentable over ‘859 in view of Ching above. From the combination of Simon, Ching, and ‘859, it would be obvious to combine Simon, Ching, and ‘859 with the teachings of Makino for the same reason that it is obvious to combine Ching and Makino as discussed in the 35 U.S.C. 103 rejection of claims 1-2, 6-11, and 13-14 above. From the combination of Simon, Ching, Makino, and ‘859, it would be obvious to combine Simon, Ching, Makino, and ‘859 with the teachings of Aygan for the same reason that it is obvious to combine Ching and Makino with Aygan as discussed in the 35 U.S.C. 103 rejection of claims 3-5 above. Therefore, the combination of ‘859 with Simon, Ching, Makino, and Aygan was obvious before the effective filing date of the claimed invention, so instant claims 1 and 3-5 are obvious variations of claim 3 in ‘859.
Conclusion
All claims are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jeffrey Lawrence Bellah whose telephone number is (571)272-1024. The examiner can normally be reached M-Th, 7:30-5 ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JEFFREY BELLAH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683