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 .
DETAILED ACTION
Status of the Claims
Claims 1-2, 5, 9, 11, 16-18, 20-21, 33-34, 37, 42-44, 47, 52, 65 and 67 are pending and the subject of this FINAL Office Action.
Claim Interpretations
The independent claims only require “a programmable DNA binding unit,” which encompasses anything that can bind DNA. Yet, the only example disclosed in dCas. Thus, Applicants are strongly encouraged to claim their invention.
New Grounds of Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. § 102 that form the basis for the rejections under this section made in this Office action:
(A) A person shall be entitled to a patent unless –
(1)the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention; or
(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-2, 5, 9, 11, 16-18, 20-21, 33-34, 37, 42-44, 47, 52, 65 and 67 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by Tan et al, Engineering of high-precision base editors for site-specific single nucleotide replacement, Nature Communications volume 10, Article number: 439 (2019).
As to claims 1-2, 5, 9, 11, 16-18, 20-21, 33-34, 37, 42-44, 47, 52, 65 and 67, Tan teaches a composition, comprising a plurality of protein complexes, wherein each of the plurality of protein complexes comprises a transposome and a programmable DNA binding unit capable of specifically binding to a binding site on a target double-stranded DNA (dsDNA) (Fig. 1), wherein the transposome comprises a transposase, a first adaptor and a second adaptor (Fig. 1), and wherein the binding site for each of the plurality of protein complexes is different from each other (para. 0540), and linker is XTEN (Fig. 1).
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New Grounds of Rejection - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-2, 5, 9, 11, 16-18, 20-21, 33-34, 37, 42-44, 47, 52, 65 and 67 are rejected under 35 U.S.C. § 103 as being unpatentable over STEEMERS (US20230279385, effective filing 08/18/2020), in view of Tan et al, Engineering of high-precision base editors for site-specific single nucleotide replacement, Nature Communications volume 10, Article number: 439 (2019).
It would have been prima facie obvious to a person of ordinary skill in the nuclease art to substitute familiar XTEN linkers for the linkers of STEEMERS with a reasonable expectation of success.
As to claim 1, STEEMERS teaches a composition, comprising a plurality of protein complexes, wherein each of the plurality of protein complexes comprises a transposome and a programmable DNA binding unit capable of specifically binding to a binding site on a target double-stranded DNA (dsDNA) (Tn5 or Tn5 linked to dCas as shown in Figs. 11 & 14 and paras. 0314, 0317, 0400, 0418, 0426, 0463, 0539 & 0683), wherein the transposome comprises a transposase, a first adaptor and a second adaptor (Fig. 11), and wherein the binding site for each of the plurality of protein complexes is different from each other (para. 0540). STEMMERS uses a linker (Figures).
As to claim 2, STEEMERS teaches at least two of the plurality of protein complexes comprise the same transposome or wherein all of the plurality of protein complexes comprise the same transposome (para. 0336).
As to claim 5, STEEMERS teaches the first adaptor and the second adaptor in the same transposome are the same; wherein the first adaptor, the second adaptor, or both, in different transposome are different, or any combination thereof (para. 0033, for example).
As to claim 9, STEEMERS teaches the first adaptor, the second adaptor, or both, is a sequencing adaptor (para. 0536, for example).
As to claim 11, STEEMERS teaches the binding sites of at least two of the plurality of protein complexes are on the same target dsDNA, wherein:
the binding sites of at least two of the plurality of protein complexes are about 1-50000 nucleotides apart on the same target dsDNA;
the distance between the binding sites of a pair of the plurality of protein complexes is substantially the same as the distance between the binding sites of another pair of the plurality of protein complexes;
the distance between the binding sites of a pair of the plurality of protein complexes is different as the distance between the binding sites of another pair of the plurality of protein complexes; or any combination thereof (Fig. 11).
As to claim 16, STEEMERS teaches at least two of the plurality of protein complexes are capable of specifically binding to different target dsDNA (para. 0323-24, 0539, 0693).
As to claim 17, STEEMERS teaches the plurality of protein complexes are capable of specifically binding to about 2-5000 target dsDNA (para. 0323-24, 0539, 0693).
As to claim 18, STEEMERS teaches the transposase is Tn5 transposase, Tn7 transposase, mariner Tc1-like transposase, Himar1C9 transposase, or Sleeping Beauty transposase (Fig. 11).
As to claim 20, STEEMERS teaches the programmable DNA binding unit comprises a nuclease-deficient CRISPR associated protein (dCAS protein) and a guide RNA (gRNA) capable of specifically binding to the binding site of the target dsDNA (Fig. 11).
As to claim 21, STEEMERS teaches the transposome is associated with the programmable DNA binding unit via a linker connecting the transposase and the dCAS protein (Fig. 11).
As to claim 33, STEEMERS teaches reaction mixture, comprising
a composition comprising a plurality of protein complexes, wherein each of the plurality of protein complexes comprises a transposome and a programmable DNA binding unit capable of specifically binding to a binding site on a target double-stranded DNA (dsDNA), wherein the transposome comprises a transposase, a first adaptor and a second adaptor, and wherein the binding site for each of the plurality of protein complexes is different from each other (claim 1, above); and
sample nucleic acids suspected of comprising one or more target dsDNA (fig. 11).
As to claim 34, STEEMERS teaches reaction mixture comprising a DNA polymerase, dNTPs, or a combination thereof and a plurality of dsDNA fragments each comprising the first adaptor and the second adaptor of one of the plurality of protein complexes at each terminus respectively (para. 0536).
As to claim 37, STEEMERS teaches the sample nucleic acids comprise eukaryotic DNA, bacterial DNA, viral DNA, fungal DNA, protozoa DNA, or a combination thereof; wherein the target dsDNA is genomic DNA, mitochondrial DNA, plasmid DNA, or a combination thereof (para. 0640, for example); and
wherein the sample nucleic acids are from a biological sample, a clinical sample, an environmental sample, or a combination thereof, wherein the biological sample comprises stool, sputum, peripheral blood, plasma, serum, lymph nodes, respiratory tissue, exudates, bodily fluid, or a combination thereof (para. 0639).
As to claim 42, STEEMERS teaches method for generating a sequencing library, comprising:
contacting a composition with a sample suspected of comprising a plurality of target double-stranded DNA (dsDNA) to form a reaction mixture, wherein the composition comprises a plurality of protein complexes, wherein each of the plurality of protein complexes comprises a transposome and a programmable DNA binding unit capable of specifically binding to a binding site on a target double-stranded DNA (dsDNA), wherein the transposome comprises a transposase, a first adaptor and a second adaptor, and wherein the binding site for each of the plurality of protein complexes is different from each other (claims 1 and 11, above);
incubating the reaction mixture to generate a plurality of dsDNA fragments each comprising the first adaptor and the second adaptor of one of the plurality of protein complexes at each terminus respectively (Fig. 11); and
amplifying the plurality of dsDNA fragments with primers capable of binding to the adaptors at the termini of the dsDNA fragments to generate a sequencing library (e.g. P5 and P7 primers or A14 and B15 primers on adaptors; Fig. 11 and paras. 0022, 0119, 0206, 0212-13, 0228-29, 0383).
As to claim 42, STEEMERS teaches each of the primers is about 5-80 nucleotides in length (id).
As to claim 44, STEEMERS teaches amplifying the plurality of dsDNA fragments with the primers is carried out using polymerase chain reaction (PCR) (id.)
As to claim 47, STEEMERS teaches the sample comprises eukaryotic DNA, bacterial DNA, viral DNA, fungal DNA, protozoa DNA, or a combination thereof;
wherein the plurality of target dsDNA comprises genomic DNA, mitochondrial DNA, plasmid DNA, or a combination thereof; and
wherein the sample is, or is derived from, a biological sample, a clinical sample, an environmental sample, or a combination thereof (claim 37, above).
As to claim 52, STEEMERS teaches generating the plurality of target dsDNA from a plurality of target RNA with a reverse transcriptase or wherein the plurality of target dsDNA comprises target dsDNA generated from target RNA with a reverse transcriptase (para. 0365).
As to claim 65, STEEMERS teaches the plurality of protein complexes and the plurality of target dsDNA are present in the reaction mixture at a molecular ratio of about 2:1 to about 2,000:1 (Fig. 11 shows two protein complexes per single DNA; see also paras. 0472-73; Example 5 uses ).
As to claim 67, STEEMERS teaches labeling one or both ends of one or more of the plurality of dsDNA fragments (para. 0669ff). The claims fail to define “label,” so it can be anything such as a barcode.
STEEMERS does not explicitly teach the linker is XTEN.
However, XTEN linkers are regularly used in the same and similar applications as STEEMERS. For example, Tan teaches
We hypothesized that the positioning on the target sequence of the Cas9 protein relative to the deaminase domain (i.e., their physical distance) and the rigidity of the connection between these two domains of the base editor determine the width of the editing window, and hence the precision of the base editor. In previous studies, a 16 amino acid (aa) flexible linker (XTEN) has been identified as the best compromise between editing efficiency and specificity16. Using l-canavanine selection in yeast17, we first investigated the effects of length and rigidity of the linker between APOBEC1 and nCas9 (Cas9 nickase) on base editing precision and efficiency when targeting several sites in the Can1 gene (Fig. 1; Supplementary Figure 1) that contain Cs within the activity window of the base editor BE3 (ref. 16). l-Canavanine is a highly toxic analog of the proteinogenic amino acid arginine, and mutations inactivating the uptake protein Can1 confer resistance to canavanine. We used an inducible base editor construct, determined the optimal induction time, and then tested 10 different rigid linker sequences (containing the amino acid proline that, due to its secondary amine, confers conformational rigidity) in comparison to the commonly used XTEN flexible linker (Supplementary Figures 1 and 2). Consistent with previous reports16, the base editor BE3 (containing the XTEN linker) allowed editing at all Cs within a window of nine nucleotides (Fig. 1; Supplementary Figure 3). Omission of the linker sequence or use of a very short rigid linker (i.e., the 3 aa linker PAP) abolished editing nearly completely. Interestingly, rigid linkers of 5–7 aa made editing substantially more precise, with the seven aa linker PAPAPAP largely restricting editing to positions −15 and −16 (Fig. 1). Longer linkers resulted in reduced editing accuracy, suggesting that a seven aa rigid linker is optimal.
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(pg. 2; Fig. 1). Thus, it is clear that XTEN linkers are obvious substitutes for the linkers of STEEMERS, with known benefits.
New Grounds of Rejection - Double Patenting- Obvious Type
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Instant claims 1-2, 5, 9, 11, 16-18, 20-21, 33-34, 37, 42-44, 47, 52, 65 and 67 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over conflicting claims 1-20 of U.S. Patent Application No. 18558052, in view of Tan et al, Engineering of high-precision base editors for site-specific single nucleotide replacement, Nature Communications volume 10, Article number: 439 (2019).
The instant claims are obvious over the conflicting claims because the conflicting claims anticipate the instant claims. Specifically, the conflicting claims teach the same multi protein complex, each with transposome, adaptors and programmable DNA binding unit:
1. A composition, comprising a first protein complex and a second protein complex, wherein
the first protein complex comprises a transposome and a first programmable DNA binding unit capable of specifically binding to a first binding site on a target double-stranded DNA (dsDNA), and
the second protein complex comprises the transposome and a second programmable DNA binding unit capable of specifically binding to a second binding site on the target dsDNA;
wherein the transposome comprises a transposase and two copies of an adaptor.
2. The composition of claim 1, comprising a plurality of protein complex pairs, wherein each of the plurality of protein complex pairs comprises the first protein complex and the second protein complex, wherein
the first binding site for each of the plurality of protein complex pairs is different from each other and/or the second binding site for each of the plurality of protein complex pairs is different from each other;
wherein all of the plurality of protein complex pairs has the same transposome.
3. The composition of claim 2, wherein the target dsDNA for two or more of the plurality of protein complex pairs are different.
5. The composition of claim 2, wherein the plurality of protein complex pairs comprises about 5-3,000 protein complex pairs.
6. The composition of claim 1, wherein
the adaptor is a dsDNA or a DNA/RNA duplex, and wherein the adaptor is about 5-200 base pairs in length.
10. The composition of claim 1, wherein the first programmable DNA binding unit comprises a nuclease-deficient CRISPR associated protein (dCAS protein) and a first guide RNA (gRNA) capable of specifically binding to the first binding site of the target dsDNA; and the second programmable DNA binding unit comprises the dCAS protein and a second gRNA capable of specifically binding to the second binding site on the target dsDNA.
13. The composition of claim 10, wherein the transposase is present in a fusion protein with the dCAS protein of the first programmable DNA binding unit, the dCAS protein of the second programmable DNA binding unit, or both.
23. The composition of claim 1, wherein the second binding site is 1-50000 nucleotides upstream or downstream of the first binding site on the target dsDNA, or wherein the second binding site is 100-500 nucleotides upstream or downstream of the first binding site on the target dsDNA.
25. The composition of claim 1, wherein the distance between the first binding site and the second binding site on each target dsDNA is substantially the same, or wherein the distance between the first binding site and the second binding site on at least two target dsDNAs are different.
27. The composition of claim 1, comprising a third protein complex, wherein the third protein complex comprises the transposome and a third programmable DNA binding unit capable of specifically binding to a third binding site on the target dsDNA, optionally the third binding site is: (i) 1-50000 nucleotides upstream or downstream of the first binding site on the target dsDNA, (ii) 1-50000 nucleotides upstream or downstream of the second binding site on the target dsDNA, and/or (iii) situated between the first binding site on the target dsDNA and the second binding site on the target dsDNA.
28. A reaction mixture, comprising:
a composition comprising a plurality of protein complex pairs, wherein each of the plurality of protein complex pairs comprises a first protein complex and a second protein complex, wherein
the first protein complex comprises a transposome and a first programmable DNA binding unit capable of specifically binding to a first binding site on a target double-stranded DNA (dsDNA), and
the second protein complex comprises the transposome and a second programmable DNA binding unit capable of specifically binding to a second binding site on the target dsDNA:
wherein the transposome comprises a transposase and two copies of an adaptor:
wherein the first binding site for each of the plurality of protein complex pairs is different from each other and/or the second binding site for each of the plurality of protein complex pairs is different from each other:
wherein all of the plurality of protein complex pairs has the same transposome;
sample nucleic acids suspected of comprising the target dsDNA;
a DNA polymerase; and
a plurality of dNTPs.
36. A method for simultaneous detection of a plurality of target nucleic acids, comprising:
contacting sample nucleic acids suspected of comprising a plurality of target double-stranded DNA (dsDNA) with a plurality of protein complex pairs to form a reaction mixture, wherein
each of the plurality of target dsDNA comprises a target sequence flanked by a first binding site on the target dsDNA and a second binding site on the target dsDNA,
each of the plurality of protein complex pairs comprises a first protein complex and a second protein complex, and wherein
the first protein complex comprises a transposome and a first programmable DNA binding unit capable of specifically binding to a first binding site on a target dsDNA,
the second protein complex comprises the transposome and a second programmable DNA binding unit capable of specifically binding to a second binding site on the target dsDNA,
wherein the transposome comprises a transposase and two copies of an adaptor,
wherein the first binding site for each of the plurality of protein complex pairs is different from each other, the second binding site for each of the plurality of protein complex pairs is different from each other, or both, and
wherein all of the plurality of protein complex pairs comprise the same transposome;
incubating the reaction mixture to generate a plurality of dsDNA fragments each comprising the adaptor on both ends and a target sequence;
amplifying the plurality of dsDNA fragments with a primer capable of binding to one strand of the adaptor to generate amplification products; and
detecting the presence of target sequences in amplified products as an indication of the presence of the plurality of target dsDNA.
38. The method of claim 36, wherein the second binding site is about 1 to 50000 base pairs upstream or downstream of the first binding site, wherein the adaptor is a dsDNA or a DNA/RNA duplex, and wherein the adaptor is about 5-200 base pairs in length.
43. The method of claim 36, wherein the plurality of target dsDNA are from one or more organisms, from one or more genes, or a combination thereof; and
wherein the plurality of target dsDNA comprises bacterial DNA, viral DNA, fungal DNA, protozoa DNA, or a combination thereof.
47. The method of claim 36, further comprising generating the plurality of target dsDNA from a plurality of target RNA with a reverse transcriptase.
48. The method of claim 36, wherein contacting the plurality of target dsDNA with the plurality of protein complex pairs is carried out at about 25° C. to about 80° C.
49. (canceled)
50. The method of claim 36, wherein the plurality of protein complex pairs and the plurality of target dsDNA are present in the reaction mixture at a molecular ratio of about 2:1 to about 2,000:1 or about 2:1 to about 200:1.
55. The method of claim 36, further comprising labeling one or both ends of one or more of the plurality of dsDNA fragments.
61. The method of claim 36, wherein the first programmable DNA binding unit comprises a nuclease-deficient CRISPR associated protein (dCAS protein) and a first guide RNA (gRNA) capable of specifically binding to the first binding site of the target dsDNA; and the second programmable DNA binding unit comprises the dCAS protein and a second gRNA capable of specifically binding to the second binding site on the target dsDNA; and
wherein the transposase is present in a fusion protein with the dCAS protein of the first programmable DNA binding unit, the dCAS protein of the second programmable DNA binding unit, or both.
66. The method of claim 36, wherein amplifying the plurality of dsDNA fragments does not use any primer other than the primer capable of binding to one strand of the adaptor.
Thus, the conflicting claims anticipate the instant claims because the conflicting claims contain the same transposome-programmable DNA binding unit (i.e. dCas) composition and method of using it to add adaptors in a targeted way to nucleic acids of interest.
Conflicting claims do not explicitly teach the linker is XTEN.
However, XTEN linkers are regularly used in the same and similar applications as STEEMERS. For example, Tan teaches
We hypothesized that the positioning on the target sequence of the Cas9 protein relative to the deaminase domain (i.e., their physical distance) and the rigidity of the connection between these two domains of the base editor determine the width of the editing window, and hence the precision of the base editor. In previous studies, a 16 amino acid (aa) flexible linker (XTEN) has been identified as the best compromise between editing efficiency and specificity16. Using l-canavanine selection in yeast17, we first investigated the effects of length and rigidity of the linker between APOBEC1 and nCas9 (Cas9 nickase) on base editing precision and efficiency when targeting several sites in the Can1 gene (Fig. 1; Supplementary Figure 1) that contain Cs within the activity window of the base editor BE3 (ref. 16). l-Canavanine is a highly toxic analog of the proteinogenic amino acid arginine, and mutations inactivating the uptake protein Can1 confer resistance to canavanine. We used an inducible base editor construct, determined the optimal induction time, and then tested 10 different rigid linker sequences (containing the amino acid proline that, due to its secondary amine, confers conformational rigidity) in comparison to the commonly used XTEN flexible linker (Supplementary Figures 1 and 2). Consistent with previous reports16, the base editor BE3 (containing the XTEN linker) allowed editing at all Cs within a window of nine nucleotides (Fig. 1; Supplementary Figure 3). Omission of the linker sequence or use of a very short rigid linker (i.e., the 3 aa linker PAP) abolished editing nearly completely. Interestingly, rigid linkers of 5–7 aa made editing substantially more precise, with the seven aa linker PAPAPAP largely restricting editing to positions −15 and −16 (Fig. 1). Longer linkers resulted in reduced editing accuracy, suggesting that a seven aa rigid linker is optimal.
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(pg. 2; Fig. 1). Thus, it is clear that XTEN linkers are obvious substitutes for the linkers of conflicting claims, with known benefits.
Prior Art
The following prior art, among many, also teaches Tn-dCas systems to target multiple sites: US20230235393; Goshayeshi et al, CRISPR/dCas9-mediated transposition with specificity and efficiency of site-directed genomic insertions, The FASEB Journal. 2021;35:e21359, https://doi.org/10.1096/fj.202001830RR, pblished online 01/26/2021; US 20190270984; US 20180312830; US 20200024654; US 20200190508; US 20200190487; US 20220403367; US 20220186290; US 20220243184; US 20220235379; US 20210071179; Bhatt et al., “Targeted DNA Transposition in Vitro Using a dCas9-transposase Fusion Protein” Nucleic Acids Res. Sep. 5, 2019;47(15):8126-8135; US 20220403419; US 20230056763; US 20230265420; US 20220243227.
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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/YUNG-SHENG M TSUI/ Primary Examiner, Art Unit 1684
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