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 .
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 .
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 6/23/2025 has been entered.
Claims 1-20 are pending in the application.
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 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 1, 2, 5, 7, 9-11, 13, 15, 17 and 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kumar and Chernaya (IDS), in view of Chen et al (IDS). This rejection is rewritten to address the amendment.
Claim 1 is drawn to a method for an in vitro transcription comprising a single step: generating a RNA in a cell free transcription reaction from a concatemeric double stranded rolling circle amplification (RCA) product comprising tandem repeats of a DNA sequence of interest, and the DNA sequence of interest comprises a promoter, an RNA coding region, and a transcription termination sequence, and said RCA product is devoid of any extraneous sequences that are required for propagation of a plasmid in a host cell.
Claim 10 is drawn to method of in vitro transcription comprising generating a concatemeric double stranded RCA product by RCA a DNA mini-circle comprising of DNA sequence of interest; and generating a RNA in a cell free transcription reaction from the double stranded RCA product, and the DNA sequence of interest comprises a promoter, an RNA coding region, a termination sequence, and said mini-circle DNA is devoid of any extraneous sequences that are required for propagation of a plasmid in a host cell.
Kumar and Chernaya teach a method for in vitro transcription and translation, comprising generating a double stranded RCA product comprising of tandem repeats of expression sequence; and generating a RNA (cell free transcription) from the double stranded RCA product in a cell free expression system, wherein the template sequence comprises a promoter, an open reading frame (RNA coding sequence), a ribosomal binding site and a translational termination sequence (see page 638, 1st col., lines 1-6, 12-15). The dsRCA product taught by Kumar and Chernaya comprises tandem repeats of expression sequence, which meets the limitation of “concatemeric ds RCA product.”
The teaching from Kumar and Chernaya differs from the claimed method from the starting template is plasmid DNA instead of DNA sequences of tandem repeats that is devoid of extraneous sequences for propagation of a plasmid in a host cell, or mini-circle DNA that devoid of extraneous sequences for propagation of a plasmid in a host cell.
Chen et al. teach a method of amplifying nucleic acids in cell free biosynthesis using a modified plasmid lacking typical genetic sequences needed for plasmid selection and replication in bacteria as a template (see page 6, 4th paragraph). Chen et al. teach using streamlined templates offers multiple benefits including elimination of any extraneous sequence that may silence the expression of the sequence of interest; more cost effective due to production of a larger quantity of an expression cassette with less material, a statistical increase in fidelity of the final product and no need for extensive purification (see page 7, 1st paragraph). Chen et al. demonstrated RCA product generated from minimal template DNA is bioactive (see example 1 and 2). Chen et al. teach the short expression cassette include an eukaryotic promoter; a sequence encoding an intact gene or fragment thereof, and a transcription termination sequence, but does not contain unnecessary genetic material which is solely used for selection and replication of a plasmid, and by minimizing bacterial genetic material that has no value inside a eukaryotic cell, it is possible to generate high concentrations of high quality, bioactive DNA molecules (see page 12, 3rd paragraph, lines 1-3 and 6-10).
It would have been obvious to an ordinary skilled in the art to replace the plasmid template used in the RCA method taught by Kumar and Chernaya with short expression cassette taught by Chen et al. The ordinary skilled in the art would be motivated to do so because Chen et al. teach elimination of the unnecessary sequences from the template has advantage of avoiding silence of the expression of sequence of interest, more cost effective and increase in fidelity of the final product to produce high concentration of high quality bioactive DNA molecules. Replacing the plasmid template with expression sequence devoid of extraneous sequence required for plasmid propagation taught by Chen would result in an amplification produce that comprises concatemeric RCA product that comprises tandem repeats of DNA of interest. The level of skill in the art is high. Absent evidence from the contrary, the ordinary skilled in the art would have reasonable expectation of success to replace the plasmid template with a short expression cassette devoid of bacterial elements for propagation following the combined teaching from Kumar and Chernaya and Chen. Therefore, the claimed invention of claims 1, 2 and 10 would have been prima facie obvious to an ordinary skilled in the art at the time the application was filed.
Regarding claims 5 and 15, Kumar and Chernaya teach the GFP gene with a His6 tag (see page 638, 1st col., line 4-6).
Regarding claims 7 and 17, Kumar and Chernaya do not mention there is a transcription termination sequence in the DNA sequence of interest, wherein the transcription of a concatemer of DNA would result in concatemer of RNA.
Regarding claims 9 and 13, Kumar and Chernaya teach E. coli kit or rabbit reticulocyte extract is used for cell free transcription and translation (see page 638, 1st col., line 18 and line 46).
Regarding claim 11, Kumar and Chernaya teach the double stranded RCA product is used in the cell free transcription without further processing (see page 638, 1st col., lines 15-16).
Regarding claim 18, Chen et al. teach using 1 mM dNTPs in RCA reaction (see page 24, line 6).
Claim(s) 3, 4 and 14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kumar and Chernaya and Chen as applied to claims 1, 2, 5, 7, 9-11, 13, 15, 17 and 18 above, and further in view of Bondarenko et al (The EMBO Journal, 2003, Vol. 22, No. 18, pages 4728-4737).
The teaching of Kumar and Chernaya and Chen has been discussed above. However, neither reference teach the double stranded RCA product comprises an insulator sequence.
Bondarenko et al. teach that insulator sequences can form domain boundaries and block inappropriate action of regulatory elements in eukaryotic nuclei, so that to confer position independent transcription to transgenes stably integrated into the genome (page 4728, 1st col., 1st paragraph). Bondarenko et al. designed inducible insulator sequences that functions in vivo (abstract).
It would have been obvious to an ordinary skilled in the art to include an insulator sequence in the DNA of interest because Bondarenko teaches said sequence can ensure independent transcription of the transgene. The ordinary skilled in the art would have reasonable expectation of success to incorporate said sequences into the DNA of interest rendered obvious by Kumar and Chernaya and Chen following combined teaching from Kumar and Chernaya, Chen and Bondarenko. Therefore, the claimed invention of claims 3 and 14 would have been prima facie obvious to an ordinary skilled in the art at the time the application was filed.
Regarding claim 4, since there is no meaningful limitation to the range as claimed, the teaching from Chen is considered to meet the limitation of transcription termination sequence is upstream of the promoter in the double stranded RCA product because the product is a concatemer and one transcription termination sequence is upstream of the next product (see Figure 2).
Claims 8, 12, 19 and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kumar and Chenaya and Chen, as applied to claims 1-5, 7, 9-11, 13-15, 17 and 18 above, and further in view of Nelson et al (IDS).
The teaching of Kumar and Chernaya and Chen has been discussed above. However, neither reference teach the double stranded RCA product comprise a thioated nucleotide, and the RCA is performed using a random primer mixture comprising a nucleotide analogue such as LNA, PNA, and the random primer mixture has NNatNatNatN*N.
Nelson et al. teach a method for efficient amplification of nucleic acids using partially constrained primers (see abstract). Nelson et al. teach that in vitro amplification of nucleic acid by rolling circle amplification (RCA) using primer mixtures that comprises nucleotide analogue such as LNA and PNA, and nuclease resistant nucleotide such as thioates would result in efficient amplification and increase specificity (see paragraph [0021], [0047], [0049], [0050], [0062] and [0063]). Nelson et al. also teach using random hexamers in the primer mixture, and 400µM dNTPs for such amplification method (see paragraph [0092]).
It would have been obvious to an ordinary skilled in the art that using nucleotide analogue such as LNA or PNA as primer for amplification reaction such as RCA would have the advantage of increased efficiency and specificity based on the teaching of Nelson et al. The ordinary skilled in the art would thus be motivated to use such nucleotide analogue in the method rendered obvious by Kumar and Chernaya and Chen to increase specificity and efficiency of RCA, thus provide more template for the subsequent in vitro transcription and translation reaction. The ordinary skilled in the art would also be motivated to use modified nucleotide such as thioates in the amplification reaction because such nucleotide are nuclease resistant based on the teaching of Nelson et al. Using random hexamer in primer mixture would also have been obvious in view of the teaching of Nelson et al. Therefore, the claimed invention would have been prima facie obvious to an ordinary skilled in the art at the time the application was filed.
Claims 6 and 16 are is/are rejected under 35 U.S.C. 103 as being unpatentable over Kumar and Chernaya and Chen, as applied to claims 1-5, 7, 9-11, 13-15, 17 and 18 above, and further in view of Greenleaf et al (WO2014189768, IDS).
The teaching of Kumar and Chernaya and Chen has been discussed above. However, neither reference specifically mention whether the protein produced in vitro is codon optimized.
Greenleaf et al. teach a method of display in vitro translated protein in solution or array on solid support (see abstract). Greenleaf et al. teach that the codon usage in the ORF of the DNA template for in vitro translation may be optimized for expression in the particular cell free expression system chosen for protein translation (see page 3, lines 17-20). Greenleaf et al. also teach that the DNA template may be amplified by RCA (see page 5, lines 5-13).
It would have been obvious to an ordinary skilled in the art that using codon optimized open reading frame for in vitro transcription and translation is desirable because it will increase the translational efficiency as evidenced by the teaching of Greenleaf et al. The ordinary skilled in the art would thus use codon optimized ORF in the method rendered obvious by Kumar and Chernaya and Chen to increase translation efficiency. Therefore, the claimed invention would have been prima facie obvious to an ordinary skilled in the art at the time the application was filed.
Response to Arguments
Applicant states the presence of extraneous sequence in an RCA product DNA materially affects the transcription and/or translation of the RCA product DNA in a cell free protein expression system, which is a surprising result observed by the present application. Applicant asserts the present application demonstrates that omission of extraneous sequence required for propagation of a plasmid unexpectedly enhance the yield of IVTT reaction. Applicant argues that there is no teaching from Kumar and Chen teaches such result. Applicant argues nothing in Chen suggests a concatemerized, rolling circle amplification product of the plasmid of Chen would be useful in a method of IVTT, or such a product would be more effective in transcribing RNA in IVTT as claimed. Applicant argues that Chen only disclose use of a small circular expression cassette in the method disclosed. Applicant argues that all of the methods taught by Chen utilize the small circular expression cassette, and optimization is achieved by using small circular expression cassette to achieve better transcription and translation. Applicant argues the larger RCA product which contains tandem repeats of the DNA sequence of interest would nullify the advantages of the vectors of Chen. Applicant argues the “bioactive” RCA product of Chen is indeed the small circularized plasmid. Applicant argues that neither Chen or Kumar suggests that there would be any advantage or reason to modify the vector of Kumar with the vector described in Chen in a method of IVT as claimed. Applicant argues that mere substitution the vector of Kumar with the expression cassette of Chen would not result in the RCA concatemer of Applicant’s claim. Applicant argues that due to the size of the Chen expression cassette, it cannot be considered a concatemer. Applicant argues that the fact that Chen teaches a concatemeric vector may be produced following RCA does not make it obvious to combine the teaching of Kumar and Chen because the input products are entirely distinct, so that there would not be reasonable expectation of success when using the concatemer of Chen with the method of Kumar.
The above argument has been fully considered but deemed unpersuasive. Applicant’s characterization of Chen is incorrect because following rolling circle amplification, the resultant product is a concatemer dsRCA product that comprises tandem repeats of a DNA sequence of interest, this aspect is shown in Figure 2 as set forth below.
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The subsequent steps of cleavage and recircularization is for the purpose of cell delivery, which is one embodiment of the application of the nucleic acid produced by RCA amplification. As discussed in the rejection and the OA mailed on 10/18/2024, Chen discusses that the nucleic acid product may be further processed in a manner to facilitate its intended use following amplification which is not limited to cellular delivery (page 7, 4th paragraph, and 8, 2nd paragraph). Kumar already demonstrated in vitro transcription and translation of RCA product, starting from a plasmid, which result in high throughput, takes less time, and can be accomplished in a single tube. Since Chen teaches removing unnecessary components of the plasmid vector for producing dsRCA concatemerized is advantageous, it would have been obvious to an ordinary skilled in the art to use the small circular DNA devoid of plasmid sequence as the starting material to produce concatemerized dsRCA and followed by IVTT processing as taught by combined teaching from Kumar and Chen. With regard to the argument directed to unexpected result, Applicant is reminded that the method only recite a single step of generating a RNA in a cell free transcription reaction from a concatemeric ds RCA product. The combined teaching from Kumar and Chen renders this step obvious (for reason discussed above), there is no further limitation for alleged unexpected results. With regard to the argument that the input products are entirely distinct between Kumar and Chen, Applicant is reminded that the RCA product of Kumar and Chen differs for removing of plasmid propagation sequences. There is no reason to support the notion that the concatemer taught by Kumar following RCA is “entirely” different from the concatemer taught by Chen (see figure above) following RCA. There is no evidence why the concatemer taught by Chen (lack of plasmid propagation sequence) cannot be in vitro transcribed into RNA. Therefore, the above rejection is still considered proper and thus maintained.
The declaration under 37 CFR 1.132 filed on 9/17/2025 is insufficient to overcome the rejection of claims 1-20 based upon Kumar and Chernaya and Chen as set forth in the last Office action for following reasons.
The declaration states that Kumar and Chen do not disclose a method of in vitro transcription including generating a transcription reaction from a concatemeric double stranded rolling circle RCA product comprising tandem repeats of a DNA sequence of interest because Chen does not teach the resulting concatemer may be used for transcription according to the claimed methods. The declaration states that Chen does not provide any indication for in vitro transcription in a cell free system, a minicircle construct would be beneficial since Chen teaches that the minicircle construct is for improvements in in vivo expression. The declaration states that neither Chen nor Kumar provide any indication that production of an RCA product may be increased by removing extraneous sequences and using a minimal construct. The declaration states that the present application demonstrates that RCA product from a minicircle construct increased product yield as compared to from plasmid construct, as shown in Figure 9. The declaration states the repeated emphasis in Chen is that smaller nuclei acids are preferable for transfection because they are more efficiently transfected, and is more efficiently expressed inside the cell. The declaration alleges that the Chen’s disclosure of a concatemeric vector is not inherently capable of being used in the transcription method of Kumar, and nor it would have been reasonable to expect that the methods of Kumar would be suitable for use with such a concatemeric vector because Chen does not provide any reason to complete the additional work required to develop a minicircle construct for rolling circle amplification that the method demonstrated by Kumar would potentially benefit from. The declaration also alleges the reaction product of Kumar does not need any improvement so there is no reason to remove unneeded bacterial sequences. The declaration cites paragraph [0028] from Chen to demonstrate that Chen’s teaching is irrelevant to the in vitro transcription and translation method of Kumar.
The above statements in the declaration does not provide sufficient reason for why the concatemeric double stranded DNA generated by Chen cannot be used for in vitro transcription method of Kumar. Applicant is reminded that the method of claim 1 only comprises a single step of “generating a RNA in a cell free transcription reaction,” wherein the starting material of the cell free transcription reaction is “a concatemeric double stranded RCA product comprising tandem repeats of a DNA sequence of interest.” The rest of the “wherein” clause does not provide further limitation to the claimed method, but rather the starting material, the double stranded RCA product, being devoid of any extraneous sequence that are required for propagation of a plasmid in a host cell. At the time of filing, cell free transcription of a double stranded RCA product would have been routine experimentation as evidenced by the teaching from Kumar. There would not have been any unpredictability for simply generating a RNA from said double stranded DNA even when sequence that encodes plasmid propagation is removed because such sequences are not required for cell free transcription. Applicant picked only teachings from Chen that discusses advantage of using smaller constructs for transfection but failed to consider the teaching from Chen as a whole. Considering the totality of the teaching from Chen, it is directed to optimization the in vitro RCA system to produce a cell free system for large scale nucleic acid production, using streamlined expression cassette templates, highly specific for random primers, high-fidelity polymerases, and a minimalistic buffer system (page 6, 2nd paragraph). Chen further discusses that the nucleic acid product may be further processed in a manner to facilitate its intended use following amplification, including detection, identification or sequencing, cellular transfection, each requires different processing accordingly (page 7, 4th paragraph), and the degree of modification or processing following the cell free amplification step is dependent upon the intended use for the product which may have different forms (page 8, 2nd paragraph). Regarding the argument directed to Chen does not teach additional work for to develop a minicircle construct for rolling circle amplification, Applicant is reminded that the claimed method does not recite any step of generating a minicircle construct for rolling circle amplification. Regarding the argument that the product taught by Kumar does not need improvement, this is not relevant because it is the combined teaching from Chen and Kumar that renders the step of generating a RNA in a cell free system, wherein the starting material comprises concatemeric double stranded DNA (the RCA process is not part of the claim limitation). For reasons discussed above, the obviousness rejection is still considered proper and therefore maintained.
Double Patenting
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 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); 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 nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 10077459. Although the claims at issue are not identical, they are not patentably distinct from each other because they both drawn to methods of in vitro transcription that using a RCA product amplifying a sequence that does not have bacterial original of replication. The method steps claimed in claim 1 and 9 of the ‘459 patent anticipates the method steps of claims 1 and 10 from the present application. Therefore, they are not patentably distinct from each other.
Dependent claims 2-8 and 10-20 from ‘459 patent recite same limitation as claims 2-9 and 11-20 of the present application.
Response to Arguments
This rejection is maintained for same reason because Applicant did not point out any error or file a TD in response to the above rejection.
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/CELINE X QIAN/Primary Examiner, Art Unit 1637