DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
This action is written in response to applicant’s correspondence received February 24, 2025. Claims 25-26, 32, 35, 37-39-55 were amended in the claim set filed February 05, 2026. Claims 1-24, 27-31, 33-34, and 36 are cancelled. Accordingly, claims 25-26, 32, 35, 37-39-55 are currently pending and under consideration.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 25, 26, 32, 35, 40-43, and 50-53 are rejected under 35 U.S.C. 103 as being unpatentable over Xu et al (WO 2006/047183 A2; Published Date: May 04, 2006), in view of Yang et al (A ligation-independent cloning method using nicking DNA endonuclease; BioTechniques, 2010, 49(5):817-821), Hegedus et al (Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis; NAR, 2009, 37(17):e112), and Gunnarsson et al (Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA-DNA hybrids in complex samples; Analytical Biochemistry, 2006, 350:120-127).
Regarding claim 25, Xu teaches “a method for preparing a plasmid (pUC19) comprising a target DNA strand having at least one nicking endonuclease recognition site on each of both ends, wherein the same strand of the target DNA strand is cleaved by a nicking endonuclease that recognizes said nicking endonuclease recognition site. (pages 24 and 25, and Figure 4C). Xu teaches “analyzing the pUC19 cleavage products by electrophoresis on polyacrylamide gel containing 7M urea indicated that the single-stranded DNA fragments were smaller than 150 nucleotides in size (FIG. 4C)” (pg. 25, paragraph 2). This teaching is interpreted as Xu positively teaching a plurality of single-stranded DNS with different molecular weights. Additionally, Xu teaches figure 4C and analysis of the pUC19 cleavage products by electrophoresis.
However, Xu does not teach step (1) cloning a double-stranded DNA because Xu discloses using a commercially available pUC19 plasmid nor wherein the single-stranded target DNA is at least 200 nucleotides in length.
Yang et al teaches “Using nicking DNA endonuclease (NiDE), we developed a novel technique to clone DNA fragments into plasmids. We created a NiDE cassette consisting of two inverted NiDE substrate sites sandwiching an asymmetric four-base sequence, and NiDE cleavage resulted in 14-base single-stranded termini at both ends of the vector and insert (i.e., a nicking endonuclease recognition site on both ends). This method can therefore be used as a ligation-independent cloning strategy to generate recombinant constructs rapidly. In addition, we designed and constructed a simple and specific vector from an Escherichia coli plasmid back-bone to complement this cloning method. By cloning cDNAs into this modified vector, we confirmed the predicted feasibility and applicability of this cloning method.” (Abstract and Figure 1). Yang et al further teaches the NiDE method has successfully cloned inserts (i.e., single-stranded target DNA) of 714 bp (e.g., Venus), 282bp (e.g., bFos), 711 bp (e.g., mLumine), 1407 bp (e.g., PS1), which are more than 200 nucleotide in length (pg. 820, col. 3, para. 3).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have cloned the plasmid for use in Xu’s method by implementing the ligation-independent strategy as taught by Yang et al because it would have merely amounted to a simple combination of known prior art elements that merely performs the same function as it does separately (e.g., the method of Yang et al generates a plasmid DNA comprising a single-stranded DNA having at least one nicking endonuclease recognition site on each of both ends of the single-stranded DNA, and the method of Xu uses this plasmid DNA for cleavage to obtain desirable single-stranded DNA). One would have been motivated to have done so for the advantage of cloning desirable single-stranded DNA sequences, especially more than 150 nucleotides in length, into the vector of Yang et al for subsequent cleavage using the method of Xu et al as opposed of cleaving fixed or undesirable single-stranded DNA sequences limited at 150 nucleotides in length from commercially available plasmids including pUC19 taught by Xu et al as an exemplary example. One would have had a reasonable expectation of success in doing so because both Yang et al and Xu et al teach methods of using nicking endonucleases to cleave nucleotide sequences from a double-stranded plasmid (step B in Figure 1 illustrated below, and pg. 24-25, respectively). See MPEP 2143(I)(A)
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However, Xu does not teach steps (3)-(5) adding a denaturing agent, denaturing the single-stranded target DNA, and performing gel electrophoresis to separate and recover the denatured single-stranded target DNA. In contrast, Xu teaches analyzing the single-stranded target DNA by gel electrophoresis on poly-acrylamide gel containing 7M urea (pg. 25, line 18).
Hegedus et al teaches cleaving double-stranded genomic DNA using a sequence-specific double-strand cleaving endonuclease SmaI to obtain 9.1 kb fragments (Fig. 3, lanes 1 and 3), as well as using a nicking endonuclease Nb.Bpu10I to obtain single-stranded DNA of this 9.1 kb fragment (Fig. 3, lanes 2, 4, and 5) under heat denaturing or urea denaturing conditions and visualized in agarose gel (pg. 4, col. 1). In addition, Hegedus et al. teaches denaturation of single stranded target DNA samples prior to loading onto a gel: “Before loading the DNA samples on the gels, either 5 μl DNA (0.1–1 µg) solution was added to 25 μl urea–LB [0.5 mg/ml bromephenol blue (Sigma), 8 M urea (Sigma), 1% (v/v) NP-40 (Calbiochem), 1mM Tris pH 8] or when DNA was embedded into agarose plugs, the blocks were soaked into freshly prepared 8 M urea solution/TE at room temperature for 45 min. These samples were either loaded without denaturation, or were heat-denatured at 80°C for 5 min and then loaded on the same gel.” (section: Sample preparation for urea-agarose gel electrophoresis). Hegedus et al. further teaches “[n]on-denaturing gel electrophoretic analysis. Lane 1, and lanes 3–4: 8573 bp ds PCR product and the separated complementary strands, respectively, cut out from the first gel (from lane 1 and 3, respectively) and re-run directly without heat denaturation. Lane 2: the excised block of the ds fragments of panel A lane 2 was heat denatured then allowed to renature (as described in ‘Materials and Methods’ section)).” This teaching of Hegedus et al is interpreted as teaching a separation step of target single-stranded DNA.
In addition, Gunnarsson et al. teaches cleaving double-stranded genomic phage DNA using a sequence-specific double-strand cleaving endonuclease BanI and a nicking endonuclease N.BstNBI to obtain single-stranded DNA which is visualized in poly-acrylamide gels with 7M urea in the presence of denaturing agent glycerol (pg. 122, col. 1, section “site-specific single-strand breaks” and “first dimension”; and pg. 125, col. 1).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the gel electrophoresis step in Xu’s method with teachings taught by Hegedus et al and Gunnarsson et al because it would have merely amounted to a simple substitution of known gel electrophoresis methods that merely serve the same purpose, e.g., separate DNA strands for visualization and characterization. One would have been motivated to have done so for the advantage of implementing a “separation system [that] can be very useful in applications requiring the separation of the complementary DNA strands in an unexpectedly broad size-range, opening new areas of application” as taught by Hegedus et al (pg. 1, col. 2, para. 2). One would have had a reasonable expectation of success in doing so because the methods of Xu et al, Hegedus et al, and Gunnarsson et al are directed to cleavage of single-stranded DNA from double-stranded DNA, and denaturing the cleavage products by performing the same actions for subsequent characterizations.
Regarding claim 26, Xu in view of Hegedus et al. teaches separation (cutting) of target pieces of single-stranded DNA by separating means. Further it would have been obvious for one of ordinary skill in the art to cut/separate out a target in order to perform additional testing and analyze the targets, as demonstrated by Hegedus et al. and discussed above.
Regarding claim 32, Hegedus et al. teaches nondenaturing agarose gel containing no denaturing agent. (Hegedus et al. Standard and urea/heat-denaturing agarose gel electrophoresis).
Regarding claim 35, Xu teaches “as judged by electrophoresis in 1.5% agarose gels.” (pg. 25, first paragraph). Additionally, Hegedus et al. teaches agarose gels (Fig. 3).
Regarding claims 40-43, the obviousness of modifying Xu’s method with the cloning strategy of Yang et al is discussed above as applied to claim 25. Further, Yang et al teach wherein at least one nicking endonuclease recognition site is Nt. BbvCI that has seven bases in the recognition site (Fig. 1B and Fig. 2C).
Regarding claims 50-52, Gunnarrson et al. teaches the denaturing agent being glycerol and also urea, as discussed above. The motivation to substitute urea for glycerol would be to substitute one known denaturing agent for another known denaturing agent that is directed to the same purpose. Both urea and glycerol perform the same function and would be expected by one of ordinary skill in the art to behave in the same way and have the same results. The recitation “at least 50 volume % glycerol” includes 100% glycerol. Therefore, the use of glycerol as the denaturing agent reads on this limitation.
Regarding claim 53, the MPEP recites “2144.05: a prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are merely close. Titanium Metals Corp. of America v. Banner, 778 F.2d 775, 783, 227 USPQ 773, 779 (Fed. Cir. 1985).” As discussed above, Gunnarrson et al. teaches that 7 M urea is used as a denaturing agent. Therefore, the 7 M of urea is considered to read on the required 6 M urea as it is considered to perform the same way and be close.
Claims 37-39 are rejected under 35 U.S.C. 103 as being unpatentable over Xu et al (WO 2006/047183 A2; Published Date: May 04, 2006), in view of Yang et al (A ligation-independent cloning method using nicking DNA endonuclease; BioTechniques, 2010, 49(5):817-821), Hegedus et al (Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis; NAR, 2009, 37(17):e112), and Gunnarsson et al (Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA-DNA hybrids in complex samples; Analytical Biochemistry, 2006, 350:120-127) as applied to claim 25, and further in view of Ó'Fágáin et al (Gel-Filtration Chromatography, Chapter 2, Methods and Protocols, Methods in Molecular Biology, 2017, 1485:15-25).
Regarding claims 37-38, the obviousness of modifying Xu’s method with the cloning strategy of Yang et al, and the obviousness of modifying Xu’s method with gel electrophoresis strategies of Hegedus et al and Gunnarsson et al are discussed above as applied to claim 25,
However, neither reference teach gel column chromatography.
Ó'Fágáin et al teaches gel-filtration chromatography. Ó’Fágáin et al teaches “One of the principal advantages of gel-filtration chromatography is that separation can be performed under conditions specifically designed to maintain the stability and activity of the molecule of interest without compromising resolution” (pg. 20, section 3. Applications of Gel-filtration chromatography). Ó’Fágáin et al teaches “Gel-filtration chromatography has for many years been used to separate various nucleic acid species such as DNA, RNA, and tRNA as well as their constituent bases, adenine, guanine, thymine, cytosine, and uracil.” (pg. 22, section 3.3 Separation of Nucleic Acids and Nucleotides).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have motivated Xu’s method by incorporating a gel-filtration chromatography step as taught by Ó'Fágáin et al because it would have merely amounted to a simple substitution of known nucleic acid purification techniques (from poly-acrylamide gel to gel-filtration columns) known in the art to serve the same purpose. One would have been motivated to have done so for the advantage of avoiding undesired side-products or products of similar lengths that are not able to be resolved in gel extractions, as well as avoiding gel extraction clean-up procedures. One would have had a reasonable expectation of success in doing so because gel-filtration chromatography is a well-known alternative nucleic acid purification technique in the art.
Regarding claim 39, the obviousness of modifying Xu’s method by incorporating gel-filtration chromatography taught by Ó'Fágáin et al is discussed above as applied to claims 37-38. Ó’Fágáin et al further teaches “Group separation can be used, for example, to effect buffer exchanges within samples, for desalting of labile samples prior to concentration and lyophilization, to remove phenol from nucleic acid preparations and to remove inhibitors from enzymes (see, for example, [25]).” (pg. 24, section 3.8 Group Separations). This teaching is interpreted as Ó’Fágáin et al envisioning desalination prior to separation.
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Xu’s method with a desalination step prior to concentration and lyophilization because it would have merely amounted to a simple combination of prior art elements that performs the same function as it does separately (gel-filtration column separating nucleic acid based on size and desalination removing undesired additives in buffer or residual enzymes from endonuclease reactions). One would have been motivated to have done so for the advantage of removing phenol from nucleic acid preparations and inhibitors from enzymes as taught by Ó’Fágáin et al (pg. 24, section 3.8 Group Separations). One would have had a reasonable expectation of success in doing so because so because it would have been Ó'Fágáin et al teaches a method of nucleic acid purification using gel-filtration chromatography with a desalination step.
Claims 44, 45, 48, 49, 54, and 55 are rejected under 35 U.S.C. 103 as being unpatentable over Xu et al (WO 2006/047183 A2; Published Date: May 04, 2006), in view of Yang et al (A ligation-independent cloning method using nicking DNA endonuclease; BioTechniques, 2010, 49(5):817-821), Hegedus et al (Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis; NAR, 2009, 37(17):e112), and Gunnarsson et al (Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA-DNA hybrids in complex samples; Analytical Biochemistry, 2006, 350:120-127) as applied to claim 25, and further in view of Zhang (US 8697359 B1; Published Date: Apr 15, 2014).
Regarding claims 44 and 45, the obviousness of modifying Xu’s method with cloning methd of Yang et al and gel electrophoresis separation strategies of Hegedus et al and Gunnarsson et al are discussed above as applied to claim 25.
However, neither reference teach the step of binding a guide RNA and wherein the nicking endonuclease is a D10A mutant of Cas9.
Zhang teaches: a nicking endonuclease d10A mutant of Cas9. Additionally, Zhang teaches “For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand).” (Zhang, Section 18). The efficiency is about 50% of nuclease (i.e., regular Cas9 without D10 mutation) in hESCs.” (Zhang, section 19).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Xu’s method to use a Cas9 nickase as taught by Zhang because it would have merely amounted to a simple substitution of nicking endonuclease (Nt.CviPII to Cas9 nickase) that serve the same purpose to yield predictable results. One would have been motivated to have done so for the advantage of nicking nucleic acids in human embroyonic stem cells as demonstrated by Zhang using double nickases Cas9 and two single guide RNAs targeting different strands. One would have had a reasonable expectation of success in doing so because Zhang teaches using nickase Cas9 to target double-stranded DNA.
Regarding claims 48 and 49, the obviousness of modifying Xu’s method with cloning methd of Yang et al and gel electrophoresis separation strategies of Hegedus et al and Gunnarsson et al are discussed above as applied to claim 25.
However, neither reference teach “wherein a guide RNA or a guide DNA binds to the sequence-specific double-stranded cleaving endonuclease recognition site”, and “wherein the sequence-specific double-stranded cleaving endonuclease is Cas9 or Argonaute.”
Zhang teaches “FIG. 1 shows a schematic model of the CRISPR system. The Cas9 nuclease from Streptococcus pyogenes (yellow) is targeted to genomic DNA by a synthetic guide RNA (sgRNA) consisting of a 20-nt guide sequence (blue) and a scaffold (red). The guide sequence base-pairs with the DNA target (blue), directly upstream of a requisite 5′-NGG protospacer adjacent motif (PAM; magenta), and Cas9 mediates a double-stranded break (DSB) ˜3 bp upstream of the PAM (red triangle).” (Zhang, Brief Description of the Drawings).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Xu’s method to use a double-stranded endonuclease Cas9 as taught by Zhang because it would have merely amounted to a simple substitution of known endonucleases (Nt.CviPII nickase to Cas9 endonuclease) to serve the same purpose. One would have been motivated to have done so for the advantage of creating a double-stranded break, mimicking the strategy taught by Hegedus et al and Guinnarsson et al using a double-stranded endonuclease in combination with a nicking endonuclease to generate single-stranded target DNA fragments. One would have had a reasonable expectation of success in doing so because Hegedus et al and Guinnarsson et al teach successful results of single-stranded DNA generation using double-stranded endonucleases.
Regarding claims 54 and 55, Xu teaches the method according to claim 25. Xu teaches a method utilizing a vector having at least one nick endonuclease recognition site on each of both ends of a cloning site. Therefore, when discussing claims 21 and 22, Xu does not teach a “kit” but does teach the individual components that could be assembled and labeled a kit. For the purposes of examination, it will state that Xu does not teach a “kit.” However, it is known that a “kit” is merely a sum of parts capable of being used in a given method.
Zhang teaches “In one aspect, the invention provides kits containing any one or more of the elements disclosed in the above methods and compositions” (Zhang, section 27). Additionally, as previously discussed, Zhang teaches a method of using at least one nicking endonuclease recognition site on one end of a cloning site and at least one sequence-specific double-strand cleaving endonuclease recognition site on the other end of the cloning site.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have created a kit utilizing the components taught by Xu and the kit components taught by Zhang because a kit is merely a collection of parts for a given method. One would have been motivated to have done so because a kit would have made performing the method taught by Xu in view of Zhang possible and the individual components would be required for the method to be performed. Xu and Zhang are directed to similar methods that require the individual components of the claimed invention; therefore, it would have been obvious to someone to combine these individual pieces and utilize them together in view of the methods described.
Claims 46 and 47 are rejected under 35 U.S.C. 103 as being unpatentable over Xu et al (WO 2006/047183 A2; Published Date: May 04, 2006), in view of Yang et al (A ligation-independent cloning method using nicking DNA endonuclease; BioTechniques, 2010, 49(5):817-821), Hegedus et al (Separation of 1–23-kb complementary DNA strands by urea–agarose gel electrophoresis; NAR, 2009, 37(17):e112), and Gunnarsson et al (Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA-DNA hybrids in complex samples; Analytical Biochemistry, 2006, 350:120-127) as applied to claim 25, and further in view of Asselbergs et al (Creation of a Novel, Versatile Multiple Cloning Site Cut by Four Rare-Cutting Homing Endonucleases, BioTechniques, 1996 20(4):558-562).
Regarding claims 46 and 47, the obviousness of modifying Xu’s method with cloning methd of Yang et al and gel electrophoresis separation strategies of Hegedus et al and Gunnarsson et al are discussed above as applied to claim 25.
However, Xu does not teach “consisting of restriction enzymes and meganucleases or TALEN” and “wherein the meganuclease is I-CeuI, I-SceI, PI-PspI, or PI-SceI”.
Asselbergs teaches meganucleases. “The novel polylinker includes sites for four of these endonucleases. PI-Seel, or VDE (14), is spliced out of the VMA ATPase of Saccharomyces cerevisiae (3,16) and has been expressed as a separate enzyme in E. coli (6,7). 1-Ppol (14,18) stems from the intron of the extrachromosomal nuclear rDNA of Physarum (10,13). 1-Ceul (14) is the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos” (Introduction).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the meganucleases taught by Asselbergs in the method of utilizing sequence-specific double-stranded cleaving endonuclease recognition sites taught by Xu in view of Zhang (as previously discussed) because “these endonucleases” (meganucleases taught by Asselbergs) “are involved in the insertion of mobile genetic elements, a process termed “homing”” (Asselbergs, introduction). Insertion of genetic elements is a goal of Xu and it would have been obvious to have used Asselbergs invention. Xu is directed to a method utilizing meganucleases and Asselbergs teaches meganucleases. Therefore, it would have been obvious to combine the method taught by Xu with the meganucleases taught by Asselbergs.
Response to the Arguments
Applicant’s remarks received on February 24, 2025, have been fully considered but they are not persuasive for at least the following reasons.
(1) Applicant argues that “Xu is not directed to the problem addressed by the present invention” (pg. 14 of Remarks, para. 6), “none of these three secondary references offers a solution that is solved by the present invention” (pg. 16 of Remarks, para. 3).
In response to Applicant’s argument (1), “[a] reference is analogous art to the claimed invention if: (1) the reference is from the same field of endeavor as the claimed invention (even if it addresses a different problem)” (emphasis added) (see MPEP 2141.01(a)(I)). Accordingly, Xu or secondary references need not see the identical problem addressed in a prior reference to be motivated to apply its teachings, and the prior art must be considered for what it teaches, and it is not limited to the context of its specific examples. All of the cited art are from the same field of endeavor as the claimed invention: Xu and secondary references, Hegedus et al and Gunnarsson et al, all disclose a method of generating single-stranded DNA (ssDNA) using nicking endonucleases and double-stranded endonucleases that recognize specific sites at defined positions on a double-stranded plasmid and visualizing cleaved ssDNA products on gel electrophoresis. A combination of their teachings offers a solution to the problem addressed by the claimed invention.
(2) Applicant argues that “Xu or these secondary references does not have a goal of providing such at homogenous, uncontaminated sample of the single-stranded target DNA of at least 200 nucleotides in length” (pg. 15 of Remarks, para. 2; and pg. 16 of Remarks, para. 2), and “a skilled person would not have an expectation of success achieving this goal” (pg. 15 of Remarks, para. 2).
In response to Applicant’s argument (2), MPEP 716.04(I) discloses “[e]stablishing long-felt need requires objective evidence that an art recognized problem existed in the art for a long period of time without solution”. The specification discloses four techniques with a common goal of a homogenous, uncontaminated sample of a single-stranded target DNAs ([0002]). In fact, the fourth technique taught by Miura et al (CRISPR/Cas9-based generation of knockdown mice by intronic insertion of artificial microRNA using longer single-stranded DNA; Scientific Reports, 2015, 5:12799; IDS received on: 08/30/2019, NPL Cite No: 4) discloses a method termed “in vitro Transcription and Reverse Transcription” that provides ssDNAs of 434 bases long (pg. 3, para. 1). The teachings of Miura et al demonstrates that the goal addressed by the claimed invention, or long-felt need, has been satisfied by another before the invention by the inventor. (see Newell Companies v. Kenney Mfg. Co., 864 F.2d 757, 768, 9 USPQ2d 1417, 1426 (Fed. Cir. 1988))
In addition, if the prior art as a whole teaches some suggestion to combine the elements, it is not required that these elements be combined for the same motivation as the Applicant's stated goal of “providing a homogenous, uncontaminated sample of single-stranded target DNA of at least 200 nucleotides in length” (see MPEP 2141.02). The fact that Applicant clones a plasmid DNA comprising the single-stranded target DNA (ssDNA) in contrast to Xu’s method utilizing a readily, commercially available pUC19 plasmid does not alter the conclusion that the proposed modifications (cloning a plasmid DNA comprising a longer ssDNA, and cutting out the cleavage products from an electrophoresis gel) would be prima facie obvious for the reasons discussed in the 35 U.S.C. 103 rejection above. See In re Lintner, 173 USPQ 560.
In addition, Xu et al explicitly demonstrates that nicking a plasmid pUC19 can yield ssDNA, albeit less than 150 nucleotides. This teaching establishes the foundational feasibility of deriving ssDNA from double-stranded plasmid using nicking endonuclease recognizing specific sites at each of both ends of the ssDNA. With this feasibility established, a person ordinary skill in the art would have been motivated to optimize parameters including ssDNA product length, and extraction strategies for additional characterizations. Hegedus et al and Gunnarsson et al both teach that longer ssDNA fragments (up to 9.1kb) can be obtained from double-stranded DNA via a combination of restriction enzymes digestion, nicking endonucleases treatment, and electrophoresis separation (denaturing and non-denaturing gels). The combination of these references addresses the limitations observed in Xu et al with reasonable predicted outcomes (see discussion above in 35 U.S.C. 103 rejection).
(3) Applicant argues that “there is no motivation in Xu to prepare a plasmid DNA…having at least one nicking endonuclease recognition site on each of both ends” (pg. 15 of Remarks, para. 3), “there is no teaching, suggestion or motivation in Xu to clone a double-stranded DNA having a single-stranded target DNA of at least 200 nucleotides in length” (pg. 15 of Remarks, para. 4), “Xu does not contemplate or mention the step of cloning…” (pg. 15 of Remarks, para. 5), “the pUC19 plasmid of Xu is not suitable for the production of the single-stranded target DNA…that is the goal of the method of the present claims” (pg. 16 of Remarks, para. 1).
In response to applicant's argument (3), the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992) (see MPEP 2144 (I)), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, a person ordinary skill in the art would have been motivated to modify the ssDNA-generating method of Xu incorporate a cloned plasmid using the method taught by Yang et al. One would have been motivated to have done so for the advantage of obtaining ssDNA with desirable lengths as opposed to using a commercially-available pUC19 plasmid where the enzyme recognition sites’ positions are fixed. Following combination of teachings from both references, one would have incorporated appropriate recognition sites for nicking endonucleases and double-stranded cleaving endonucleases at defined positions, and such modification merely represents a combination of prior art elements to yield predictable results according to their established functions (see MPEP 2143 (I)(A)).
In addition, references do not have to explicitly suggest to combine the teachings. Rather, establishing a prima facie case of obviousness requires a clear articulation of a rationale for combining the teachings of the references (see MPEP 2144), and such rationale has been provided in the rejection above.
In summary, Applicant’s response is not sufficient to rebut the prima facie case of obviousness, and the rationale to combine prior art elements according to known methods to yield predictable results is explained in both 35 U.S.C. 103 rejection and Response to Arguments. Accordingly, the rejection under 35 U.S.C. 103 is maintained.
CONCLUSION
No claims are allowable.
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.
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QIWEN SU-TOBON
Examiner
Art Unit 1636
/NEIL P HAMMELL/
Supervisory Patent Examiner, Art Unit 1636
Prosecution Insights