DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 04 August 2026 has been entered.
Claim Status
3. Claims 46, 48-50, 53-64 and 66-69 are pending and have been examined herein.
Claim Interpretation
4. Claim 46 recites “each recognition site comprising a sequence of a minimum of about 10 nucleotides up to about 80 nucleotides.” Claim 59 recites “each recognition site comprising a sequence of a minimum of about 17 nucleotides up to about 80 nucleotides.”
In the reply of 07 November 2025, Applicant states:
“the claim phrase "a minimum of about 10 nucleotides up to about 80 nucleotides," when read in light of the specification defining the term "about," as acknowledged by the Office Action, as "containing the stated number of bases or base-pairs with a variation of 0-10% around the value (X 10%)" informs those skilled in the art with reasonable certainty about the length of the claimed recognition sites-a minimum of 9 and up to 88 nucleotides (where "about 10" contains 9-11 nucleotides and "about 80" contains 72-88 nucleotides, respectively). Therefore, one skilled in the art would readily recognize that "a minimum of about 10 nucleotides up to about 80 nucleotides" does not encompass 7 or 8 nucleotides as alleged in the Office Action. Similarly, a skilled artisan would recognize that recognition sites of claims 59-64 reciting "a minimum of about 17 nucleotides up to about 80 nucleotides" contains between 16 and 88 nucleotides (where "about 17" contains 15.3-18.7 nucleotides and "about 80" contains 72-88 nucleotides, respectively).”
Consistent with Applicant’s arguments, the definition in the specification at para [0047] for “about” with respect to polynucleotides is considered to apply to the endonuclease recognition site. Thus, claims 46, 48, 53-58, 66 and 68 are considered to require that the recognition site for the endonuclease consists of a minimum of 9 nucleotides up to 88 nucleotides and claims 59-64, 67 and 69 are considered to require that the recognition site for the endonuclease consists of a minimum of 16 nucleotides up to 88 nucleotides.
New Claim Rejections - 35 USC § 112(a) – New Matter
5. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 46, 48-50, 53-64 and 66-69 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new matter rejection.
The disclosure as originally filed does not provide basis for the recitations in the claims of “wherein the 3' and 5' ends of the bridge oligo hybridize to at least 7 nucleotides at or immediately adjacent to the first and second recognition sites” (see claims 46 and 59); or the recitation in claims 66 and 69 of “wherein the 3' and 5' ends of the bridge oligo hybridize to at least 8 nucleotides at the first and second recognition sites”; or the recitation in claims 68 and 69that the bridge oligo has “towards” the 3’ end (claim 68) or 5’ end (claim 69) at least the first three nucleotides of the first or second recognition site.
The response of 04 August 2026 states “Support for the amendments can be found throughout the subject specification, e.g., at page 12, line 21 to page 13, line 24, page 14, lines 7-20, page 15, lines 3-16, page 15, line 31 to page 16, line 10, Figures 5-8, and in the claims as originally filed.”
However, the cited portions of the disclosure do not provide basis for these recitations in the amended and new claims and there is no explanation as to how the teachings in the cited portions of the disclosure provide basis for these recitations.
The disclosure (para [0071]; paragraph numbering herein is with respect to the published application) teaches:
“When the gRNA binds to the recognition site, the Cas9 endonuclease creates a double stranded break in the double stranded genetic material at three nucleotides toward the 5′ side of the NGG sequence on the non-complementary strand, i.e., starting from the 5′ end and going towards the 3′ end of the recognition site, Cas9 endonuclease makes a double stranded break between the third and the fourth nucleotide.”
Thereby, the disclosure suggests that when the cleavage step is accomplished using a Cas9 endonuclease, there will be 3 nucleotides of the recognition site present on the cleaved genomic DNA. However, this teaching does not indicate that when the cleaving step is performed using any endonuclease, a bridge oligo is used that includes sequences at the 5’ and 3’ ends (or “towards” the 5’ and 3’ ends) that will hybridize to at least 7 nucleotides of the first and second recognition sites (as encompassed by claims 46 and 59) or 8 nucleotides of the first and second recognition sites (claims 66 and 67) or 3 nucleotides of the first or second recognition sites (claims 68 and 69).
Similarly, the disclosure in the specification at p. 13 lines 7 to p. 16, line 26 (i.e., the description of Figures 5-8) are limited to methods wherein the endonuclease is Cas9 endonuclease. These cited portions of the specification teach that there will be three nucleotides from the first and/or second recognition sites remaining in the target genomic region following cleavage with Cas9 endonuclease. However, none of the claims are limited to methods in which the endonuclease is Cas9 endonuclease.
For example, the disclosure at para [0087], with respect to Figure 7, states “Target genomic region has, at the end towards the first recognition site, the first three nucleotides of the first recognition site and has, at the end towards the second recognition site, the first three nucleotides of the second recognition site.”
Again, this disclosure is limited to methods in which the cleaving step is accomplished using Cas9 endonuclease (i.e., “The first gRNA binds to the first recognition site on the top strand and the Cas9 endonuclease cuts the genomic DNA three nucleotides downstream of the 5′ end of the first recognition site”, para [0087]).
If Applicant maintains that the originally filed disclosure provides basis for the amended claims, Applicant should explain how the cited teachings in the specification and Figures 5-8 provide basis for each of the recitations set forth in the claims.
See MPEP 2163 II at “(b) New Claims, Amended Claims, or Claims Asserting Entitlement to the Benefit of an Earlier Priority Date or Filing Date under 35 U.S.C. 119, 120, 365, or 386” which states:
“To comply with the written description requirement of 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, or to be entitled to an earlier priority date or filing date under 35 U.S.C. 119, 120, 365, or 386, each claim limitation must be expressly, implicitly, or inherently supported in the originally filed disclosure.”
Modified Claim Rejections - 35 USC § 103
6. 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.
Claim(s) 46, 48-50, 53-64 and 68-69 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stemeers et al (U.S. 20130316917; cited in the IDS) in view of Wang et al (U.S. 20180002706) and Zeiner et al (U.S. 20140357523)
Stemeers teaches a method for capturing a target genomic region from genetic material, the method comprising: cleaving a target genomic region at a 5’ end and a 3’ end with one or more endonucleases, including endonucleases that have recognition sites of 7 base pairs and rare cutters; denaturing the cleaved genetic material to form single-stranded target DNA; and capturing the single-stranded target DNA using a selector probe having sequences at the 5’ and 3’ ends that hybridize to the 5’ and 3’ ends of the single-stranded target DNA (see, e.g., para [0095], [0111], [0117] and Figure 3).
“As a first step in the circularization reaction, the DNA sample is digested by restriction enzymes to generate target fragments with defined ends. The digested DNA sample can be then denaturated to allow the selector to hybridize to the restriction fragments and template ligation to the vector oligonucleotide, forming single-stranded circular DNA molecules. This step can be performed in a least two methods. In a first method the ends of a targeted restriction fragment hybridize to the appropriate selector probe, and the ends become juxtaposed to the vector oligonucleotide guided by the selector probe. Next, a ligase joins the restriction fragment to the vector oligonucleotide generating a circular DNA strand.”
As shown in Figure 3A, the 5’ and 3’ ends of the selector probe are target-specific and thereby hybridize to the 5’ and 3’ ends of the single-stranded target DNA (Figure 3B). Thus, the selector probe of Stemeers constitutes a “bridge oligo.” Note that in Figure 3A, the “Sector probe” is the bottom single-stranded DNA molecule with the “Target specific ends” as shown below:
PNG
media_image1.png
172
482
media_image1.png
Greyscale
Regarding the limitation that the bridge oligo is a single stranded oligonucleotide, Stemeers (para [0109]) teaches “selector probes comprise hybridization tags, e.g., target-complementary end-sequences, joined by a general linking sequence adapted to ligate templates and to direct circularization of target nucleic acids.” The selector probe (i.e., bridge oligo) having sequences at the 3' and 5' ends that hybridize to the sequences at the 3' and the 5' ends, respectively, of the single stranded target genomic region is thereby a single stranded oligonucleotide.
Stemeers does not teach methods that comprise cleaving the target genomic region with an endonuclease that has a recognition site that has a minimum length of at least 9 nucleotides (i.e., “about 10 nucleotides” - claims 46, 48-50 and 53-58) or a minimum length of 16 nucleotides (i.e., “about 17 nucleotides” - claims 59-64), particularly wherein the endonuclease is a programmable endonuclease, and specifically is a Cas9 endonuclease.
However, Stemeers does teach using rare cutting endonucleases (para [0095]).
Further, Wang teaches methods of cleaving target genomic DNA using Cas9 endonuclease (e.g., para [0004]). Wang teaches that “Commonly used restriction enzymes have six or eight bp recognition sequences, which have an occurrence frequency of one in every 4096 or 65536 bp, respectively, in a random sequence” (para [0065]). It is disclosed that this can be problematic when a restriction endonucleases are not suitable when a restriction site is not located in a target region or when multiple restriction sites are present in a target sequence due to the frequency at which the site may occur (para [0065]). It is disclosed that CRISPR-associated protein-9 (Cas9) cleavage can overcome these problems since this endonuclease is programmable and has a recognition site of about 20 bp (para [0071] and [0109]). For instance, Wang (para [0071]) states:
“The CRISPR-associated protein-9 (Cas9) is an endonuclease that cleaves a double-stranded DNA target site guided by a single guide RNA (sgRNA). A sgRNA is composed of a fusion of target-specific CRISPR-related sequence (crRNA) that is from the target sequence and a trans-activating CRISPR-related RNA (tracrRNA) sequence that is from the bacterial CRISPR system. A crRNA, also known as protospacer, is a sequence of usually 20-nucleotides.”
Wang concludes that Cas9 nuclease is highly efficient and can be used as a restriction enzyme to cleave DNA (para [0107]).
Additionally, Zeiner teaches methods of fragmenting genomic DNA and detecting target polynucleotides comprising cleaving a target nucleic acid with CRISPR-associated Cas proteins and a plurality of, including at least two, Cas9-associated guide RNAs, wherein one guide RNA directs cleavage at the 5’ end of a target DNA and a second guide RNA directs cleavage at the 3’ end of the target DNA (e.g., para [0003], [0033], [0049], [0074] and [0088]). It is disclosed that the Cas9-associated guide RNAs may each be specific for a different, pre-defined, site in genomic DNA (para [0063]).
Zeiner (para [0049]) states:
“The guide RNAs used in the method may be designed so that they direct binding of the Cas9-gRNA complexes to pre-determined cleavage sites in a genome. In certain cases, the cleavage sites may be chosen so as to release a fragment that contains a region of unknown sequence, or a region containing a SNP, nucleotide insertion, nucleotide deletion, rearrangement, etc.”
Zeiner further teaches isolating, amplifying and/or sequencing the DNA fragments generated by the Cas9 cleavage (para [0054] and [0090]).
In view of the teachings of Wang and Zeiner, 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 method of Stemeers so as to have cleaved the target genomic DNA with a Cas9-gRNA endonuclease in place of a restriction endonuclease with a recognition site of 6- or 7-bp. One would have been motivated to have done so for the benefits disclosed by Wang and Zeiner of providing a method with high level of specificity of cleavage since the Cas9-gRNA endonuclease system recognizes target sequences of 20-bp (i.e., a minimum of about 10 or about 17 nucleotides) and thereby the recognition site occurs less frequently in the genome and the target recognition site can be easily customized for a target genomic region based on the selection of the single stranded guide RNA.
Regarding the recitation in the amended claims that “the 3' and 5' ends of the bridge oligo hybridize to at least 7 nucleotides at or immediately adjacent to the first and second recognition sites,” Stemeers teaches that the hybridization tag is complementary to a portion of the target, including sequences sharing 99% or 100% complementarity with the target sequence (e.g., para [0077]) and teaches that “a hybridization tag can comprise at least about… 15 nucleotides, at least about 20 nucleotides, at least about 25 nucleotides, at least about 30 nucleotides, at least about 35 nucleotides… and at least about 1000 nucleotides” (para [0079]).
See, for example, Figure 6, a portion of which is shown below in which the target specific ends of the selector probe hybridize to the single-stranded cleaved target DNA at the 5’ and 3’ ends, which includes sequences of the first and second recognition sites:
PNG
media_image2.png
314
352
media_image2.png
Greyscale
Accordingly, the teachings of Stemeers, when considered as a whole, suggest using selector probes (bridge oligos) in which the 3' and 5' ends hybridize to at least 7 or more nucleotides of the target sequence that includes sequences at the first and second recognition sites and nucleotides immediately adjacent to the first and second recognition sites.
Further, and particularly with respect to claims 68 and 69, modification of the method of Stemeers so as to have cleaved the target genomic DNA with a Cas9-gRNA endonuclease system generally would have resulted in cleavage products having at least 3 nucleotides of the recognition sequence at the 5’ end and 3 nucleotides of the recognition sequences since Cas9 endonuclease cuts genomic DNA 3 nucleotides downstream of the 5’ end of the recognition site. Accordingly, the hybridization tags at the 5’ and 3’ ends of the selector probe would have necessarily included at least 3 nucleotides that are complementary to the first and/or second recognition sites.
Regarding claims 48-50, modification of the method of Stemeers as set forth above would have resulted in a method in which the genomic DNA is cleaved with the programmable endonuclease of Cas9-gRNA endonuclease, wherein the Cas9-gRNA endonuclease comprises a first endonuclease that cuts DNA at a first recognition site based on a first RNA guide molecule having a sequence complementary to the first recognition site and a second programmable endonuclease that cuts DNA at a second recognition site based on a second RNA guide molecule having a sequence complementary to the second recognition site.
Regarding claim 53, in the embodiment disclosed by Stemeers at para [0109]), the region between the target-complementary end-sequences, including a “linking sequence” is considered to include a primer binding site sequence, since a primer can bind to this sequence.
Regarding claim 54, Stemeers teaches that the probe is attached to a biotin moiety (i.e., “biotinylated”; e.g., para [0080]).
Regarding claims 55-58, as discussed above, Stemeers teaches the embodiment in which a capture probe comprises a selector probe (i.e., bridge oligo) and a vector probe (para [0110] and Figure 3). As shown in Figure 3B I, the ends of the digested genomic DNA are indirectly ligated via ligation with the vector probe portion that is hybridized to the selector probe (bridge oligo). This results in a structure comprising a circularized single-stranded target DNA hybridized to the selector probe (bridge oligo). Thus, Stemeers teaches “ligating the free ends of the single stranded target genomic region hybridized to the bridge oligo to produce a single stranded circular target genomic region that is hybridized to the bridge oligo.” Note that steps e) and f) of claim 55 are optional and thereby need not occur. Further, step g) of analyzing the amplified target genomic region is also considered to be optional because the only amplification step recited in the claim occurs in optional step f). Alternatively, Stemeers teaches “In some embodiments, after the circularization reaction, linear sample DNA is degraded by exonucleolysis” (para [0111]. Thereby, Stemeers teaches degrading non-circularized genetic material. Stemeers teaches amplifying the circularized target DNA (e.g., para [0111] and [0114]) and also teaches sequencing the target genomic DNA (e.g., para [0006], [0016], [0060] and [0109]).
Regarding claim 56, Stemeers teaches that the circularized target DNA can be amplified by rolling circle replication, which is considered to be rolling circle amplification (e.g., para [0114] “Circular nucleic acid molecules can be amplified by a variety of methods, for example, rolling circle replication”).
Regarding claim 57, as discussed above, the analyzing step is considered to be optional since it depends on the optional amplifying step. Further, Stemeers teaches sequencing the Cas9-cleaved target genomic DNA (e.g., para [0006], [0016], [0060] and [0109]).
Regarding claim 58, Stemeers does not teach that sequencing the Cas9-cleaved target genomic DNA comprises nanopore sequencing.
However, as discussed above, Zeiner teaches sequencing the fragments generated by the Cas9 cleavage (para [0054] and [0090]), particularly using nanopore sequencing (para [0055]).
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 method of Stemeers so as to have sequenced the Cas9-cleaved target genomic DNA region since Zeiner teaches that this is an effective means for sequencing DNA, and particularly DNA generated by Cas9-gRNA cleavage.
Regarding claims 59-64, as discussed above, modification of the method of Stemeers so as to have cleaved the target genomic DNA using the Cas9-gRNA endonuclease system would have resulted in a method in which the recognition site for the endonuclease is about 20 nucleotides in length, which is within the claimed minimum range of about 17 nucleotides up to about 80 nucleotides in length. Stemeers teaches that the method may be a multiplex method (e.g., para [0053], [0109] and [0113]). Stemeers also teaches the embodiment in which a capture probe (i.e., bridge oligo) comprises a selector probe and a vector probe (para [0110]). The capture probe itself also constitutes a bridge oligo. As shown in Figure 3, the vector probe portion of the capture probe (bridge oligo) is ligated to the 5’ and 3’ ends of the cleaved, single-stranded target DNA and this complex is subsequently amplified. Thus, this embodiment of Stemeers also includes a step of “capturing the plurality of target genomic regions in the single stranded form by hybridizing the plurality of target genomic region to a plurality of bridge oligos, wherein each bridge oligo comprises sequences at the 3' and 5' ends that hybridize to the 3' and 5' ends, respectively, of a target genomic region from the plurality of target genomic regions in single stranded form.”
Regarding claim 61, Stemeers teaches that the capture probe (i.e., bridge oligo) can be attached to an affinity tag, such as a biotin moiety so as to facilitate the separation of the affinity tagged nucleic acids from untagged molecules (para [0116-0117]). For instance, Stemeers states “The selector probe is ligated to the ssDNA. Biotin affinity moieties of the capture probes bind to streptavidin bound to beads. The beads are washed and unassociated nucleic acids are stringently washed from the beads. The washed nucleic acids are eluted from the beads.” (para [0117]). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have performed the method of Stemeers using a biotin-tagged selector probe / bridge oligo that was subsequently immobilized onto a solid support / streptavidin coated bead in order to have facilitated the separation of the cleaved target genomic DNA region bound to the capture probe / bridge oligo from unbound DNA and other reagents, thereby permitting the isolation of the cleaved target genomic DNA region bound to the capture probe / bridge oligo, as disclosed by Stemeers.
Regarding claims 62-64, Stemeers teaches amplifying the cleaved target genomic regions by PCR to form multiple copies of the target genomic region (e.g., para [0070], [0109], [0111] and [0113]).
Further, regarding claim 64, Stemeers teaches performing multiplex PCR using primers that are a universal primer pair and which bind to the “general primer-pair motif” present in the selector probe (e.g., Figure 3 and [0110-0111]).
Response to Remarks:
The response states: "one skilled in the art would not have been motivated to combine the cited references, where Stemeers teaches a method that "provide[s] sufficient specificity to allow analysis of unique sequences in human genomic DNA" (Stemeers, paragraph 111) and no problem or need is suggested in the art to give a skilled artisan a reason to combine Stemeers with Wang and Zeiner. “
These arguments have been fully considered but are not persuasive. First, there is no requirement for Stemeers to suggest modification of the method disclosed therein. As set forth in MPEP 2141 IIC "The proper analysis is whether the claimed invention would have been obvious as of the relevant time to one of ordinary skill in the art after consideration of all the facts." Further, MPEP 2143 provides examples of rationales that may support a conclusion of obviousness, including "(G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art
reference or to combine prior art reference teachings to arrive at the claimed invention." Herein, the prior art of Wang and Zeiner provide the motivation to perform the cleaving step using the Cas9-gRNA endonuclease systems in place of the restriction endonucleases used in the method of Stemeers. Wang and Zeiner teach that the Cas9-gRNA endonuclease system provides the benefit of a higher specificity of cleavage since the endonuclease system recognizes target sequences that are longer in length, such that the target recognition site occurs less frequently in the genome, thereby increasing the specificity of cleavage and the target recognition site can be easily customized for a target genomic region based on the selection of the single stranded guide RNA.
The response states:
“There is no teaching or suggestion in the combined cited references or the art at the time of the current application that a method for capturing target genomic regions employ a single stranded bridge oligo wherein the 3' and 5' ends of the bridge oligo hybridize to at least 7 nucleotides at the first and second recognition sites.”
However, the rejection is based on the combination of Stemeers, Wang and Zeiner and not on the individual references alone. As discussed in the rejection, modification of the method of Stemeers so as to have used the Cas9-gRNA endonuclease systems of Wang and Zeiner would have resulted in a method in which the selector probe (bridge oligo) hybridizes to the single-stranded cleaved target DNA at the 5’ and 3’ ends, which region includes sequences of the first and second recognition sites. Wang teaches that the recognition site for the Cas9-gDNA endonuclease is about 20bp in length. Also Stemeers teaches that the selector probe comprises a hybridization tag at the 5’ and 3’ ends, which hybridization tags share, e.g., 99% or 100% complementarity with the target nucleic acid (para [0077]) and are of 10 or 15 or 20 etc. nucleotides in length (e.g., para [0079]). Thus, modification of the method of Stemeers so as to have used the Cas9-gDNA endonuclease for the cleavage reaction in place of a restriction endonuclease that recognizes 6 or 7 nucleotides would have resulted in a method in which the selector probe has at its 5’ and 3’ ends hybridization tags that comprise at least 7 nucleotides complementary to at least 3 nucleotides of the first or second recognition sites and complementary to sequences immediately adjacent to the first and second recognition sites. Note that Cas9 endonuclease cuts the genomic DNA three nucleotides downstream of the 5′ end of the first recognition site so that 3’ nucleotides of the recognition site remain on the target genomic DNA at the cleavage site. Also note that claims 46, 48-50, 53-64, 68 and 69 recite “wherein the 3' and 5' ends of the bridge oligo hybridize to at least 7 nucleotides at or immediately adjacent to the first and second recognition sites.” These claims do not require that the bridge oligo hybridizes to at least 7 nucleotides at the first and second recognition sites, as argued by Applicant.
Additionally, regarding claims 59-64, these claims do not require that the bridge oligo is a single-stranded oligonucleotide. Rather, as broadly recited, claims 59-64 encompass methods in which the bridge oligo is a double-stranded oligonucleotide. As discussed in the rejection as it pertains to claims 59-64, the double-stranded capture oligonucleotide of Stemeers comprising the single-stranded selector probe and the vector oligonucleotide (Figure 3A) can also be viewed as a “bridge oligo.” Figure 3 of Stemeers shows that the capture oligonucleotide binds to and captures a “plurality of target genomic regions in the single stranded form by hybridizing the plurality of target genomic region to a plurality of bridge oligos, wherein each bridge oligo comprises sequences at the 3' and 5' ends that hybridize to the 3' and 5' ends, respectively, of a target genomic region from the plurality of target genomic regions in single stranded form.”
The response states:
“Stemeers, the only reference mentioning capturing nucleic acids, uses random, restriction enzyme site-based cutting of genomic DNA and "selection" of a target genomic region by capturing and testing the resultant random genomic DNA pieces for the presence of a "selected" target region. In contrast, it is the claimed method that enables capture of a target genomic region specifically selected (prior to performing the method) by using an endonuclease with a first and second recognition site comprising a sequence of a minimum of about 10 nucleotides up to about 80 nucleotides and a single stranded bridge oligo designed to hybridize to at least 7 nucleotides at the first recognition site and the second recognition site of the selected target genomic region that enables specific and efficient capture of the selected target genomic region.”
These arguments have also been fully considered but are not persuasive. The recitations in the amended claims of “capturing a selected target genomic region” and “cleaving the selected target genomic region” do not distinguish the claimed method over the method suggested by the combined prior art. Stemeers teaches “Nickases include endonucleases that recognize a specific recognition sequence in a double-stranded nucleic acid, and cut one strand at a specific location relative to the recognition sequence, thereby giving rise to single-stranded breaks in the double-stranded nucleic acid” (para [0097]). Accordingly, the cleavage step in Stemeers is not random. Also, throughout the Stemeers reference it is made clear that the method is one for the selective enrichment of a nucleic acid (see, e.g., Title “Selective enrichment of nucleic acids” and para [0003]). The method of Stemeers also encompasses selecting a target genomic region which target region is cleaved and then captured using the selector probe since the method of Stemeers requires selecting a restriction endonuclease to cleave the target genomic DNA and obtaining / generating a selector probe that hybridizes to and captures the cleaved target genomic DNA.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CARLA J MYERS whose telephone number is (571)272-0747. The examiner can normally be reached M-Th 6:30-5:00 EST.
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, Wu-Cheng Winston Shen can be reached on 571-272-0731. 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.
/CARLA J MYERS/Primary Examiner, Art Unit 1682
Prosecution Insights