DETAILED ACTION
Status of the Claims
Claims 1-16, 18-19, 25, and 33 are currently pending and are examined herein.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 04/06/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specifically, amino acid sequences appear in Fig. 6A and are not labeled with SEQ ID NOs in the drawing or in the Brief Description of the Drawings.
Claim Objections
Claim 13 is objected to as being dependent upon a rejected base claim, but would be free from the prior art if rewritten in independent form including all of the limitations of the base claim and any intervening claims. Appropriate correction is required.
Claim Rejections – 35 U.S.C. 102
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 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 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 person shall be entitled to a patent unless –
(a)(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.
Tawfik et al.
Claims 1-4, 6-10, 15-16, 18-19, and 25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tawfik et al. (Nat. Biotech., 1998, 16:652-656).
Regarding claims 1-3 and 18, Tawfik discloses a composition and/or kit for methylating target DNA for transformation into a host cell, the composition comprising:
a cell-free transcription-translation mixture (e.g., partitioned aliquots of E. coli S30 extract system from Promega and S-adenosyl methionine as per the In vitro transcription/translation section on p. 655); and
at least one expression construct encoding one or more components of a methylation complex (e.g., DNA encoding for M.HaeIII as per the Experimental protocol section on pp. 655-656);
wherein the methylation complex replicates at least a portion of a methylation pattern used by the host cell on the target DNA (e.g., M.HaeIII is part of the restriction/methylation system as per the Introduction section and/or Fig. 1B).
Regarding claim 4, Tawfik discloses the above composition, wherein the host cell is a bacterial cell (e.g., from the bacterium Haemophilus influenzae as per the Preparation of DNA section on p. 655).
Regarding claim 6, Tawfik discloses the above composition, wherein the cell free transcription-translation mixture is derived from bacterial cell lysate (e.g., E. coli S30 extract system from Promega as per the In vitro transcription/translation section on p. 655).
Regarding claim 7, Tawfik discloses the above composition, wherein at least one component of the cell free transcription-translation mixture is purified (e.g., S-adenosyl methionine as per the In vitro transcription/translation section on p. 655).
Regarding claims 8 and 19, Tawfik discloses the above composition, wherein the one or more components of the methylation complex comprises a methyltransferase associated with a Type II RM system in the host cell (e.g., M.HaeIII is from a Type II RM system).
Regarding claim 9, Tawfik discloses the above composition, wherein the one or more components of the methylation complex comprises at least one methyltransferase (e.g., M.HaeIII is a methyltransferase as per the Introduction section and/or Fig. 1B).
Regarding claim 10, Tawfik discloses the above composition, wherein the at least one methyltransferase is derived from the host cell (e.g., from the bacterium Haemophilus influenzae as per the Preparation of DNA section on p. 655).
Regarding claim 15, Tawfik discloses the above composition, further comprising S-Adenosyl methionine (SAM) as a methyl donor (e.g., S-adenosyl methionine as per the In vitro transcription/translation section on p. 655).
Regarding claim 16, Tawfik discloses the above composition, further comprising a suitable methylation buffer (e.g., E. coli S30 extract system from Promega as per the In vitro transcription/translation section on p. 655).
Regarding claim 25, Tawfik discloses a method of methylating a target DNA using the kit of claim 18, the method comprising expressing the one or more components of the methylation complex in the cell-free transcription-translation mixture comprising the target DNA, wherein the methylation complex replicates at least a portion of a methylation pattern used by the host cell on the target DNA (e.g., expressing M.HaeIII methyltransferase in an E. coli S30 extract system from Promega as per the In vitro transcription/translation section on p. 655). Note that the limitation in the preamble of “for transforming into a host cell” appears to be an intended use of the methylated DNA and the claim does not reasonably require a transformation step.
Sarrade-Loucheur et al.
Claims 1-10, 15-16, 18-19, and 25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sarrade-Loucheur et al. (PLoS, 2013, 8(11):e80967).
Regarding claims 1-3 and 18, Sarrade-Loucheur discloses a composition and/or kit for methylating target DNA for transformation into a host cell, the composition comprising:
a cell-free transcription-translation mixture (e.g., NEB PURExpress in vitro transcription/translation system as per the Methyltransferase activity assays section on p. 2); and
at least one expression construct encoding one or more components of a methylation complex (e.g., DNA encoding for M1.BpuSI as per the Methyltransferase activity assays section on p. 2);
wherein the methylation complex replicates at least a portion of a methylation pattern used by the host cell on the target DNA (e.g., M1.BpuSI is part of the Type II restriction/methylation system as per the Introduction section on pp. 1-2).
Regarding claims 4-5, Sarrade-Loucheur discloses the above composition, wherein the host cell is a bacterial cell (e.g., originally isolated from Bacillus pumilus as per the Introduction section).
Regarding claim 6, Sarrade-Loucheur discloses the above composition, wherein the cell free transcription-translation mixture is derived from bacterial cell lysate (e.g., PURExpress in vitro transcription/translation system from NEB as per the Methyltransferase activity assays section on p. 2).
Regarding claim 7, Sarrade-Loucheur discloses the above composition, wherein at least one component of the cell free transcription-translation mixture is purified (e.g., S-adenosyl methionine as per the Methyltransferase activity assays section on p. 2).
Regarding claims 8 and 19, Sarrade-Loucheur discloses the above composition, wherein the one or more components of the methylation complex comprises a methyltransferase associated with a Type II RM system in the host cell (e.g., M1.BpuSI is part of the Type II restriction/methylation system as per the Introduction section on pp. 1-2).
Regarding claim 9, Sarrade-Loucheur discloses the above composition, wherein the one or more components of the methylation complex comprises at least one methyltransferase (e.g., M1.BpuSI is a methyltransferase as per the Introduction section on pp. 1-2).
Regarding claim 10, Sarrade-Loucheur discloses the above composition, wherein the at least one methyltransferase is derived from the host cell (e.g., from Bacillus pumilus as per the Introduction section).
Regarding claim 15, Sarrade-Loucheur discloses the above composition, further comprising S-Adenosyl methionine (SAM) as a methyl donor (e.g., S-adenosyl methionine as per the Methyltransferase activity assays section on p. 2).
Regarding claim 16, Sarrade-Loucheur discloses the above composition, further comprising a suitable methylation buffer (e.g., NEBuffer 1 as per the Methyltransferase activity assays section on p. 2).
Regarding claim 25, Sarrade-Loucheur discloses a method of methylating a target DNA using the kit of claim 18, the method comprising expressing the one or more components of the methylation complex in the cell-free transcription-translation mixture comprising the target DNA, wherein the methylation complex replicates at least a portion of a methylation pattern used by the host cell on the target DNA (e.g., expressing M1.BpuSI methyltransferase in the PURExpress in vitro transcription/translation system from NEB as per the Methyltransferase activity assays section on p. 2). Note that the limitation in the preamble of “for transforming into a host cell” appears to be an intended use of the methylated DNA and the claim does not reasonably require a transformation step.
Cohen et al.
Claims 1-4, 6-12, 14-16, 18-19, and 25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Cohen et al. (Protein Engineering, Design & Selection, 2004, 17(1):3-11).
Regarding claims 1-3 and 18, Cohen discloses a composition and/or kit for methylating target DNA for transformation into a host cell, the composition comprising:
a cell-free transcription-translation mixture (e.g., as per the Library selection by IVC section on p. 5); and
at least one expression construct encoding one or more components of a methylation complex (e.g., as per the Library selection by IVC section on p. 5);
wherein the methylation complex replicates at least a portion of a methylation pattern used by the host cell on the target DNA (e.g., M.HaeIII is part of the restriction/methylation system as per the Introduction section).
Regarding claim 4, Cohen discloses the above composition, wherein the host cell is a bacterial cell (e.g., from the bacterium Haemophilus influenzae as per the Introduction section).
Regarding claim 6, Cohen discloses the above composition, wherein the cell free transcription-translation mixture is derived from bacterial cell lysate (e.g., as per the Library selection by IVC section on p. 5).
Regarding claim 7, Cohen discloses the above composition, wherein at least one component of the cell free transcription-translation mixture is purified (e.g., S-adenosyl methionine as per the Library selection by IVC section on p. 5).
Regarding claims 8 and 19, Cohen discloses the above composition, wherein the one or more components of the methylation complex comprises a methyltransferase associated with a Type II RM system in the host cell (e.g., M.HaeIII is from a Type II RM system).
Regarding claim 9, Cohen discloses the above composition, wherein the one or more components of the methylation complex comprises at least one methyltransferase (e.g., M.HaeIII is a methyltransferase as per the Introduction section).
Regarding claim 10, Cohen discloses the above composition, wherein the at least one methyltransferase is derived from the host cell (e.g., from the bacterium Haemophilus influenzae as per the Introduction section).
Regarding claims 11-12 and 14, Cohen discloses the above composition, wherein the methyltransferase is mutated to enhance methylation (e.g., as per the Library selection by IVC section on p. 5).
Regarding claim 15, Cohen discloses the above composition, further comprising S-Adenosyl methionine (SAM) as a methyl donor (e.g., S-adenosyl methionine as per the Library selection by IVC section on p. 5).
Regarding claim 16, Cohen discloses the above composition, further comprising a suitable methylation buffer (e.g., as per the Library selection by IVC section on p. 5).
Regarding claim 25, Cohen discloses a method of methylating a target DNA using the kit of claim 18, the method comprising expressing the one or more components of the methylation complex in the cell-free transcription-translation mixture comprising the target DNA, wherein the methylation complex replicates at least a portion of a methylation pattern used by the host cell on the target DNA (e.g., expressing M.HaeIII methyltransferase in an E. coli S30 extract system from Promega as per the Library selection by IVC section on p. 5). Note that the limitation in the preamble of “for transforming into a host cell” appears to be an intended use of the methylated DNA and the claim does not reasonably require a transformation step.
Conclusion
Claim 33 is allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684
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