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 .
Office Action: Notice
A request for continued examination under 37 CFR 1.114, including the fee set forth in
37 CFR 1.17(e), was filed in this application after final rejection. Since this application is
eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e)
has been timely paid, the finality of the previous Office action has been withdrawn pursuant to
37 CFR 1.114. Applicant's submission filed on 2/23/2026 has been entered.
Claim Status
Claims 33, 42, and 57 have been amended (2/23/2026). Claims 2, 4-5, 8-9, 11-14, 16-17, 19-20, 24-25, 27-31, 34, 36-41, 43-44, 46-53, 55-56, 58, 60-63, 69 and 72-73 are cancelled (2/23/2026). No new matter was added. Thus, claims 1, 3, 6-7, 10, 15, 18, 21-23, 26, 32-33, 35, 42, 45, 54, 57, 59, 64-68 and 70-71 are under examination.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure
statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information
submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be
incorporated into the specification but must be submitted in a separate paper." Therefore, unless
the references have been cited by the examiner on form PTO-892, they have not been
considered.
The information disclosure statement (IDS) submitted on 2/23/2026 is being considered by the examiner.
Rejections Withdrawn
Claim Rejections - 35 USC § 102
The 102 (a) (1) and 102 (a) (2) rejection of claims 1, 3, 6, 7, 10, 15, 18, 21-23, 26, 32-33, 42, 45, 54, 57, 64-68, 70 are withdrawn in view of Applicant’s arguments (2/23/2026). Specifically, the Applicant’s argument that Abudayyeh’s programmable endonuclease cleave at predictable, sequence-specific sites and therefore do not necessarily teach the claimed use of a non-specific endonuclease to generate a random plurality of fragments, is persuasive.
Claim Rejections - 35 USC § 112 (b)
The 112(b) rejections for 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant) for claims 33, 35 and 57, are withdrawn in view of Applicant’s amendments of claim 5 for use of the term “preferably.”
New Rejections
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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, 3, 6-7, 10, 15, 18, 21-23, 26, 32-33, 42, 45, 54, 57, 64-68 and 70 are rejected under 35 U.S.C. 103 as being unpatentable over Abudayyeh et al., (WO 2018/107129 A1, published 6/14/2018), in view of Zylicz-Stachula et al., (“A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries”, Springer Nature, published 2013) and in further view of Sudol et al. (“Evaluation of a system to screen for stimulators of non-specific DNA nicking by HIV-1 integrase: application to a library of 50,000 compounds”, Antiviral Chemistry and Chemotherapy, published 2011).
Regarding claim 1, Abudayyeh teaches a nucleic acid detection method consisting of: a CRISPR system comprising an effector protein or bridge oligonucleotide and one or more guide RNAs designed to bind to corresponding target molecules or stabilized biological samples (Paragraph 4, lines 1-5) that includes a generic nucleic acid binding protein with fusion to or being operably linked to a functional domain (Paragraph 172, lines 1-5). Abudayyeh further teaches the inclusion of adaptive immune systems contain programmable endonucleases, such as Cas9 and Cpfl (Paragraph 142, lines 1-5) in order to cleave or form a first fragment or segment and a second fragment or segment (i.e., CRISPR enzyme orthologs) (Paragraph 168, lines 5-10) followed by attachment at a junction or reporter construct modified to comprise a linker or quencher to facilitate binding (Paragraph 270, lines 10-15). Additionally, Abudayyeh teaches only certain target molecules can exist because of their chemical or molecular properties, such as through size selection or exclusion, where gel beads may exclude certain species or sizes or segments from entering the beads but not others (Figures 2, 88; Paragraph 262, lines 10-15) followed by linkage via single-stranded RNA (ssRNA) or RNA oligonucleotide bridges that hybridize on each end of the RNA or nucleic acid segments to at least a portion of the DNA linkers (Paragraph 229, lines 10-20; Paragraph 230, lines 1-5).
Regarding claim 3, Abudayyeh teaches that the size selected fragments or segments or RNA lengths are in the range of 70 bp to 200 bp (Paragraph 303, lines 1-5).
Regarding claims 6 and 7, Abudayyeh teaches that the previously described method, was further explored to unveil the diversity of cleavage preferences of the various orthologs or segments of interests via a library -based approach for characterizing motifs preferred for endonuclease activity in response to collateral activity (Paragraph 512, lines 1-5). Further, Abudayyeh teaches the applicability of size-selectivity in detectable cleavage which further depended on the addition of targeted RNA fragments of segments (Figure 88; Paragraph 512, lines 10-15), followed by sequencing of depleted motifs which revealed an increase in the skew of the library over digestion time (Figure 89 A; Paragraph 512, lines 10-15).
Regarding claim 10, Abudayyeh teaches the incorporation of nucleic acid diagnostics, recognizing the ability to simultaneously detect multiple sample inputs, allowing for multiplexed detection panels or for in sample controls to ensure efficient quality control measures (Paragraph 512, lines 1-5).
Regarding claim 15, Abudayyeh teaches the incorporation of a quantum dot attached to a surface, bound to a portion of linker molecules or segments or fragments described previously via contact with programmable endonucleases (Paragraph 142, lines 1-5) via quenching of the quantum dot (Paragraph 233, lines 1-5).
Regarding claim 18, Abudayyeh teaches that a stabilized biological sample can also be a sample obtained from any organ or tissue (including a biopsy or autopsy specimen, such as a tumor biopsy) or can include a cell (whether a primary cell or cultured cell) or medium conditioned by any cell, tissue or organ; including, cells, cell lysates, blood smears, cytocentrifuge preparations, cytology smears, bodily fluids (e.g., blood, plasma, serum, saliva, sputum, urine, bronchoalveolar lavage, semen, etc.), tissue biopsies (e.g., tumor biopsies), fine-needle aspirates, and/or tissue sections (e.g., cryostat tissue sections and/or paraffin-embedded tissue sections) (Paragraph 343, lines 1-10).
Regarding claims 21 and 22, Abudayyeh teaches that a salt, such as potassium chloride (KC1), or sodium chloride (NaCl), may be included in an amplification reaction, such as PCR, in order to improve the amplification of nucleic acid fragments following formation of target segments or fragments (Paragraph 242, lines 5-10) via contact with previously described programmable endonucleases (Paragraph 142, lines 1-5) and attachment at a junction or reporter construct modified to comprise a linker or quencher to facilitate binding (Paragraph 270, lines 10-15). Abudayyeh further teaches that these biological or chemical reaction may include a cell lysis component in order to break open or lyse a cell for analysis of the materials contained within (Paragraph 243, lines 1-5).
Regarding claims 23 and 26, Abudayyeh teaches that the previously described method has applicability to detect as few as one target variant within the background of 105-106 targeted cells of a biological sample (Paragraph 394, lines 5-10). Abudayyeh further teaches that the biological sample of interest is at concentrations as low as 20 aM DNA (Figure 3; Paragraph 492, lines 15-20).
Regarding claim 32, Abudayyeh teaches the inclusion of adaptive immune systems contain programmable endonucleases, including DNAse II (i.e., Cas9 and Cpfl) (Paragraph 142, lines 1-5) in order to cleave or form a first fragment or segment and a second fragment or segment (i.e., CRISPR enzyme orthologs) (Paragraph 168, lines 5-10).
Regarding claim 33, Abudayyeh teaches the cross-linking or optically-defined treatment of the previously described stabilized biological via illuminating it with visible, ultraviolet, infrared, or other wavelengths of light such that only target molecules within the defined space or volume may be labeled by a color change (Paragraph 262, lines 15-20).
Regarding claims 42, 45 and 54, Abudayyeh teaches the use of antibodies in the previously described method via binding an antibody (Paragraph 283, lines 15-20) specific or individualized for the effector protein or bridge oligonucleotide via chemical precipitation (Paragraph 427, lines 1-3). Further, Abudayyeh teaches that one or more nucleic acid barcodes can be attached, or “tagged,” to a target molecule and/or target nucleic acid via direct (i.e., covalent or non-covalent binding of the barcode to the target molecule) or indirect (i.e., additional molecule, for example, a specific binding agent, such as an antibody (or other protein) or a barcode receiving adaptor through the previously described antibody binding (Paragraph 471, lines 15-25). Abudayyeh further teaches that affinity tags are well known (i.e., HA tag, Myc tag, Flag tag, His tag, biotin) and are coupled to an effector protein or bridge oligonucleotide, often times consisting of a biotin molecule and discrete volumes of streptavidin (Paragraph 283, lines 10-15).
Regarding claim 57, Abudayyeh teaches that the previously described method of junction or construct attachment comprises the target sequence or fragment hybridizing to one or more of the individualized probes used to identify a selection of fragments or target sequences sequentially or in a series via indication of the presence of the target within the sample (Paragraph 325, lines 1-5). Specifically, Abudayyeh teaches that the individualized probes are equipped with bridge oligonucleotides or RNA molecules allowing the detection agent to disperse and identify the presence of the target sequence of fragment via a color change (Figures 43 and 46; Paragraph 235, lines 5-10).
Regarding claims 64-68 and 70, Abudayyeh teaches that following distinguishing biological entities of interest (i.e., tissues, cells, microvesicles, biomarkers) at the oligonucleotide junction or reporter construct a sensor probe or plurality of such probes can also be used to further explore the diversity of cleavage preferences of the various Cas orthologs to characterize motifs preferred for endonuclease activity in response to activity via read pair or DNA handles for readout of uncleaved sequences (Figure 83C; Paragraph 643, lines 1-5). Further, Abudayyeh teaches that the CRISPR systems are used to screen microbial genetic perturbations and map out microbial pathways and functional networks (Paragraph 327, lines 1-5) via specialized contig sets (Table 6) via integration into the genome of a host cell upon introduction into the host cell and are capable of directing or revealing expression or orientation of the relevant genes or genes of interest (Paragraph 155, lines 15-25), including target molecules comprising loss-of-heterozygosity (LOH) markers (Paragraph 10, lines 1-3). Abudayyeh also teaches that the previously described mapping or screening technique can be used to target different nucleic acids in a single assay, allowing for detection of multiple variants of a single target (Paragraph 255, lines 5-10). Specifically, Abudayyeh teaches that the variant of interest can be targeted via immunomagnetic beads coated with antibodies to Epithelial Cell Adhesion Molecule (EpCAM) to enrich for EPCAM-expressing epithelial cells, followed by immunostaining to confirm the presence of cytokeratin and/or leukocyte antigen markers (Paragraph 418, lines 15-25). Further, Abudayyeh teaches that the previously described method for contig mapping for variant detection can be applied to screen for drug resistance in selecting an appropriate treatment regime (Paragraph 298, lines 1-5), as well as a number of clinically relevant mutations that could be detected (i.e., acute infection, disease stage) (Paragraph 300, lines 1-3).
Abudayyeh does not teach or suggest contacting a stabilized biological sample with a non-specific endonuclease to generate a random plurality of nucleic acid fragments.
Zylicz-Stachula teaches that genomics and metagenomics are currently leading research areas, with DNA sequences accumulating at an exponential rate, and although enormous advances in DNA sequencing technologies are taking place, progress is frequently limited by factors such as genomic contig assembly and generation of representative libraries (Background: Paragraph 1). Further, Zylicz-Stachula teaches that a number of DNA fragmentation methods, such as hydrodynamic sharing, sonication or DNase I fragmentation, have various drawbacks, including DNA damage, poor fragmentation control, irreproducibility and non-overlapping DNA segment representation and improvements in these limited DNA scission methods are consequently needed and conversely an alternative method for obtaining higher quality DNA fragments involves partial digestion with restriction endonucleases (REases) (Background: Paragraph 1). Further, Zylicz-Stachula teaches that they constructed a horse genomic library and a deletion derivative library of the butyrylcholinesterase cDNA coding region using a novel method, based on TaqII, Thermus sp. family bifunctional enzyme exhibiting cofactor analogue specificity relaxation (Results: Paragraph 1). Specifically, Zylicz-Stachula teaches that TspGWI, a member of the newly-designated Thermus sp. family of bifunctional REases-MTases exhibits a novel type of substrate specificity change causing much more frequent cleavage and this feature could be useful for improving genomic technologies where the observed specificity change is induced by the replacement of the enzyme cofactor SAM with its analogue, SIN, which causes a change in REase cleavage frequency that is statistically equivalent to a 5-bp to 3-bp recognition site shift (Background: Paragraphs 3-4).
Sudol teaches that in addition to activities needed to catalyse integration, retroviral integrases exhibit non-specific endonuclease activity that is enhanced by certain small compounds, suggesting that integrase could be stimulated to damage viral DNA before integration occurs (Background). Specifically, Sudol teaches that a non-radioactive, plate-based, solution phase, fluorescence assay was used to screen a library of 50,080 drug-like chemicals for stimulation of non-specific DNA nicking by HIV-1 integrase (Methods). Further, Sudol teaches that a semi-automated workflow was established and primary hits were readily identified from a graphic output (Results).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to modify Abudayyeh’s method by substituting or incorporating an endonuclease, as taught by Zylizc-Stachula and further expanded upon as being non-specific in nature, by Sudol, in order to generate a plurality of nucleic acid fragments for analysis or library preparation. The motivation to do so arises from the well-known need to obtain representative and diverse nucleic acid fragments for downstream detection and sequencing applications, as well as the recognition in the art that different fragmentation methods, including non-specific enzymatic cleavage, are interchangeable alternatives for producing such fragments. Furthermore, a person of ordinary skill in the art would have had a reasonable expectation of success in making this substitution because enzymatic fragmentation of nucleic acids using endonucleases, including non-specific cleavage, was a routine and well-understood technique, and substituting one known fragmentation approach for another would have predictably yielded a plurality of nucleic acid fragments suitable for subsequent analysis.
Applicant’s Response: The Applicant argues that Abudayyeh does not teach or disclose contacting a stabilized biological sample with a non-specific endonuclease, as required by the claims, because Abudayyeh relies on programmable, sequence-specific cleavage. The Applicant further argues that such programmable cleavage does not inherently produce a random plurality of fragments, as non-specific endonucleases would.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully and fully considered and are found to be partially persuasive, as discussed below.
While Abudayyeh teaches programmable, sequence-specific cleavage, the rejection has been modified under 35 USC 103, and no longer relies on inherency. As set forth in MPEP 2143, it is sufficient that the prior art suggests the claimed invention as a whole.
Zylicz-Stachula teaches that enzymatic fragmentation of nucleic acids using endonucleases is a known and routine technique for generating DNA fragments in library preparation workflows (Background; Results). Further, Sudol teaches that endonucleases are capable of non-specific DNA cleavage activity (Background). Accordingly, it would have been obvious to a person of ordinary skill in the art to substitute or incorporate a non-specific endonuclease into the method of Abudeyyah to obtain a plurality of nucleic acid fragments, as such substitution represents the use of a known alternative technique to achieve a predictable result (MPEP 2143, 2144). A person of ordinary skill in the art would have had a reasonable expectation of success because nucleic acid fragmentation via endonucleases, including non-specific cleavage, was well understood and routinely practiced.
Rejections Maintained
Claim Rejections - 35 USC § 103
Claims 35, 59 and 71 are rejected under 35 U.S.C. 103 as being unpatentable over Abudayyeh et al., (WO 2018/107129 A1, published 6/14/2018) in view of Zylicz-Stachula et al., (“A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries”, Springer Nature, published 2013) and in further view of Sudol et al. (“Evaluation of a system to screen for stimulators of non-specific DNA nicking by HIV-1 integrase: application to a library of 50,000 compounds”, Antiviral Chemistry and Chemotherapy, published 2011), as applied to claims 1, 3, 6-7, 10, 15, 18, 21-23, 26, 32-33, 42, 45, 54, 57, 64-68 and 70 above, and in further view of Hornung et al. (WO 2018/064229 A1, published 4/5/2018). This rejection has been modified based on Applicant amendments and argument (2/23/2026).
As discussed above, Abudayyeh teaches a nucleic acid detection method consisting of: a CRISPR system comprising an effector protein or bridge oligonucleotide and one or more guide RNAs designed to bind to corresponding target molecules or stabilized biological samples (Paragraph 4, lines 1-5) that includes a generic nucleic acid binding protein with fusion to or being operably linked to a functional domain (Paragraph 172, lines 1-5) for clinical applications, as discussed above. Further, Zylicz-Stachula teaches that they constructed a horse genomic library and a deletion derivative library of the butyrylcholinesterase cDNA coding region using a novel method, based on TaqII, Thermus sp. family bifunctional enzyme exhibiting cofactor analogue specificity relaxation (Results: Paragraph 1). And additionally, Sudol teaches that in addition to activities needed to catalyse integration, retroviral integrases exhibit non-specific endonuclease activity that is enhanced by certain small compounds, suggesting that integrase could be stimulated to damage viral DNA before integration occurs (Background).
Regarding claim 35, Abudayyeh teaches the cross-linking or optically-defined treatment of the previously described stabilized biological via illuminating it with visible, ultraviolet, infrared, or other wavelengths of light such that only target molecules within the defined space or volume may be labeled by a color change (Paragraph 262, lines 15-20).
Regarding claims 59 and 71, Abudayyeh teaches the inclusion of adaptive immune systems contain programmable endonucleases, such as Cas9 and Cpfl (Paragraph 142, lines 1-5) in order to cleave or form a first fragment or segment and a second fragment or segment (i.e., CRISPR enzyme orthologs) (Paragraph 168, lines 5-10) followed by attachment at a junction or reporter construct modified to comprise a linker or quencher to facilitate binding (Paragraph 270, lines 10-15). Specifically, Abudayyeh teaches that the individualized probes are equipped with bridge oligonucleotides or RNA molecules allowing the detection agent to disperse and identify the presence of the target sequence of fragment via a color change (Figures 43 and 46; Paragraph 235, lines 5-10). Further, Abudayyeh teaches the incorporation of nucleic acid specific binding proteins with fusion to or being operably linked to a functional domain within the amplification method (i.e., endonuclease, bridging oligonucleotides or RNA molecules) (Paragraph 172, lines 5-10).
Abudayyeh, Sudol or Zylicz-Stachula do not teach or suggest that the chemical fixative agent comprises formaldehyde, psoralen, disuccinimidyl glutarate (DSG), or ethylene glycol bis (succinimidyl succinate) (EGS) or that the biological sample can be coupled or fused to specific immunoglobulin binding proteins selected from a Protein A, G, A/G and L.
Hornung teaches a method for creating an oligonucleotide library that binds targets of interest, specifically to identify viral variants and infections (Abstract). Hornung further teaches that the stabilized biological sample or target of interest can be fixed via cross-linking to assist in maintaining the complex between the binding agent and the target (i.e.,, with an aldehyde such as formaldehyde or glutaraldehyde), precipitation (i.e., using an alcohol such as methanol, ethanol and acetone, and acetic acid), oxidation (i.e., using osmium tetroxide, potassium dichromate, chromic acid, and potassium permanganate), mercurials, picrates, Bouin solution, hepes-glutamic acid buffer-mediated organic solvent protection effect (HOPE), and freezing (Paragraph 317, lines 1-10).
Hornung also teaches that the individual oligonucleotide bridges within the attachment constructs or junction can be modified based on type and size, dependent upon steric hindrance factors between the associated target protein and the Clq protein/MAC complex or immunoglobulin binding protein selection (i.e., Protein A, Protein G, Protein A/G, Protein L combination). (Figure 8B; Figure 8C, Design 3; Paragraph 354, lines 15-20).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to modify Abudayyeh’s method, in consideration of the role of non-specific endonucleases, as taught by Sudol and Zylicz-Stachula, by using the specific fixative agents and immunoglobulin binding proteins taught by Hornung. Specifically, it would have been obvious to incorporate Hornung’s specific list of fixatives (i.e., formaldehyde) because they are well-documented in preserving biological sample integrity while maintaining accessibility for downstream molecular analyses. These fixatives provide reliable and reproducible results across a wide range of sample types, making them ideal for standardization of protocols. Further, the combinational approach of Hornung geared towards the immunoglobulin binding proteins would allow researchers to further optimize binding interactions based on a wide range of steric considerations, thereby improving detection sensitivity and specificity. There would be a reasonable expectation of success because both references focus on methods for molecular detection in stabilized biological samples. Hornung demonstrates that these fixatives, specifically, effectively preserve sample structure while maintaining molecular accessibility (Paragraph 317, lines 1-10), and the immunoglobulin binding proteins are well-characterized reagents with predictable binding properties (Paragraph 354, lines 15-20). This combination would be expected to succeed because Hornung provides detailed guidance on both fixation conditions and protein selection parameters, allowing one of ordinary skill in the art to readily implement these modifications to Abudayyeh’s method, in view of Sudol and Zylicz-Stachula.
Applicant’s Response: The Applicant asserts that Abudayyeh does not disclose all elements of amended independent claim 1. Specifically, Abudayyeh teaches programmable endonucleases like Cas9, which are specific rather than the claimed non-specific endonucleases, and does not teach contacting a stabilized biological sample to cleave into a plurality of segments. Further, the Applicant asserts that Abudayyeh fails to teach subjecting the plurality of segments to size selection to obtain ligated segments as required by amended independent claim 1. Accordingly, the Applicant argues that due to the dependency of claims 35, 59, and 71 on claim 1, as well as the inclusion of additional details that the secondary reference, Hornung does not cure, these related claims, are novel over Abudayyeh in view of Hornung.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully considered but are not found persuasive, as discussed below.
Specifically, claims 35, 59 and 71 recite additional features beyond amended independent claim 1, such as chemical fixation with specific crosslinking agents and the use of immunoglobulin binding proteins. Abudayyeh already teaches the underlying method of nucleic acid fragmentation, ligation, and detection in stabilized biological samples as described above (Paragraphs 142, 168, 243, 262, 303). Newly added reference, Zylizc-Stachula further teaches that nucleic acid fragmentation using endonucleases is a known technique for generating DNA fragments in genomic library preparation (Background; Results), and additionally, newly added reference Sudol expands on this to teach that endonucleases are capable of non-specific DNA cleavage activity (Background). Hornung supplements this disclosure by expressly teaching fixation of biological samples using aldehyde and glutaraldehyde-based crosslinking agents, as well as selection of immunoglobulin binding proteins such as Protein A, Protein G, Protein A/G, and Protein L (Hornung: Paragraphs 317, 354).
It would have been obvious to one of ordinary skill in the art to combine Hornung’s fixation and binding protein teachings with Abudayyeh’s stabilized nucleic acid detection methods to improve sample preservation, reproducibility, and detection sensitivity, as well as to incorporate known non-specific endonuclease fragmentation techniques as taught by Zylizc-Stachula and evidenced by Sudol. Specifically, Zylizc-Stachula provides guidance on enzymatic fragmentation techniques, and Sudol teaches that non-specific endonuclease activity was known in the art. Both references, in combination with Abudayyeh and Hornung, relate to molecular analysis of nucleic acids in biological samples. Specifically, Hornung teaches detailed guidance on fixation reagents and protein selection, and both references address molecular detection in stabilized biological samples. The rationale to combine is supported by KSR Int’l v. Teleflex, 550 US 398, 417 (2007), as the modifications represent routine optimization of known methods for predictable results. See MPEP 2143.
Accordingly, the combination of Abudayyeh, Zylizc-Stachula, Sudol and Hornung teaches or suggests all limitation of instant claims 35, 59, and 71. Therefore, the rejection under 35 USC 103 is maintained.
Conclusion
No claim is allowed.
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/ELIZABETH ROSE LAFAVE/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684