DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 2, 8, 14 and 20 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding Claim 2, Claim 2 recites the term “U/μg” with respect to DNase concentration. This claim is indefinite because it is unclear what the units of the denominator refer to. The unit μg may refer to the weight of circular RNA, linear RNA, linear DNA, or any combination within the reaction product as well as the total weight of the reaction product. The instant specification does not provide a definition, and the description on page 10, DNase I digestion does not provide clarity. Therefore, Claim 2 is rejected under 35 USC 112(b) for failing to distinctly claim the subject matter.
Regarding Claims 8, 14, and 20, the term “U/μg” is used again without defining what μg is in reference to within their respectively solutions as described above for Claim 2. The instant specification fails to provide clarity with respect to μg. Therefore, Claims 8, 14, and 20 are rejected under 35 USC 112(b) for failing to distinctly claim the subject matter.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 1-3, 5-7, and 9-11 are rejected under 35 U.S.C. 103 as being unpatentable over Wesselhoft, R. et. al., Nature Communications, Vol. 9, No. 2629, p. 1-10, July 6, 2018 and Goldberg, M. and Carmona, E., US 2018/0169146 A1, June 21, 2018. The rejections of Claims 2 and 3 are evidenced by England Biolabs, “A typical DNase I Reaction (M0303) V.1”, published January 17, 2015. The rejection of Claim 11 is evidenced by New England Biolabs 2, “Protocol for XRN-1 NEB M0338”, published January 2017.
Wesselhoft teaches a method where (a) products of a splint ligation reaction, comprising of circular polyribonucleotides, linear ribonucleotides, and linear polydeoxyribonucleotides, are (b) reacted with DNase for 20 minutes wherein the second digestion mixture comprises an enriched population of circular polyribonucleotides (p. 8-9, circRNA design and purification).
Wesselhoft does not teach (c) where the product of the digested mixture of step (b) is reacted with an exonuclease.
Goldberg teaches a method where (a) products of a splint ligation reaction to create circular polyribonucleotides are (c) treated with an exonuclease including Xrn-1 and Exonuclease T to removed unwanted non-circularized product for greater product purity: “non-circularized nucleic acid molecules may be digested with an RNase, e.g.,… Exonuclease T, … or XRN-1” (p. 2, [0022]); “XRN-1 exonucleases result in the highest purity of circularized product” (p. 2, [0031]).
Regarding Claim 1, it would have been obvious to one skilled in the art before the effective filing date to have performed a simple combination of Wesselhoft and Goldberg to create the method of Claim 1 by adding the exonuclease treatment taught by Goldberg to the method of Wesselhoft. Wesselhoft teaches steps (a) and (b), and Goldberg teaches steps (a) and (c). Each step is sequential and involves creating and purifying circRNA, and the steps are well known in the art as described by Wesselhoft and Goldberg. The results would be predictable because Wesselhoft and Goldberg are able to create enriched populations of circRNA. One would be motivated to perform the combination as Goldberg teaches the exonuclease digestion removes non-circularized nucleic acid molecules, the undesired product, for a higher purity circularized product. Therefore, Claim 1 is obvious over Wesselhoft and Goldberg.
Regarding Claims 2 and 3, Claim 1 is obvious over Wesselhoft and Goldberg. Wesselhoft teaches the use of DNase I from New England Biolabs: “After in vitro transcription, reactions were treated with DNase I (New England Biolabs) for 20 min” (p. 8, col 2). New England Biolabs recites the protocol for DNase I that uses 2 units of DNase I for 10 μg of RNA which is 0.2 units of DNase I per 1 μg of RNA (Steps 1 and 2) at 37°C (Step 4). Therefore, it would have been inherent to the teachings of Wesselhoft to use 0.2 units of DNase I per 1 μg of RNA at 37°C.
Regarding Claim 2, Claim 2 is rejected under 35 USC 112(b) for failing to identify the limitations of U/μg. For compact prosecution, U/μg is interpreted as units of DNase I/ μg of RNA. Wesselhoft teaches a method using 0.2 units of DNase I per 1 μg of RNA, which is within 0.1 and 1 as evidenced by New England Biolabs (Steps 1 and 2). Therefore, Claim 2 is obvious over Wesselhoft and Goldberg.
Regarding Claim 3, Wesselhoft teaches a method where step (b) is performed for 20 minutes at 37°C, which is at least 10 minutes as evidenced by New England Biolabs (Step 4). Therefore, Claim 3 is obvious over Wesselhoft and Goldberg.
Regarding Claim 5, 6 and 7, Goldberg teaches a method using a 5’-phosphate dependent exonuclease, Xrn-1 (p. 2, [0022]). Therefore, Claims 5, 6 and 7 are obvious over Wesselhoft and Goldberg.
Regarding Claim 9 and 10, Goldberg teaches a method using a 3’ exonuclease, Exonuclease T (p. 2, [0022]). Therefore, Claims 9 and 10 are obvious over Wesselhoft and Goldberg.
Regarding Claim 11, Goldberg teaches a method using XRN-1 from New England Biolabs 2: “Any remaining linear RNA in the circularization reactions was removed using the exonuclease Xrn-1 (NEB, #M0338L)” (p. 15, Example 1, [0129]). New England Labs 2 recites a protocol XRN-1 in which the reaction is incubated at 37°C for 60 minutes (Step 3). Therefore, it is inherent to the method of Goldberg to perform a digestion for at least 1 hour at a temperature of 37°C. Therefore, Claim 11 is obvious over Wesselhoft and Goldberg.
Claims 13-15, 17-19, and 21-23 are rejected under 35 U.S.C. 103 as being unpatentable over Moore, M. and Query, C., Methods in Enzymology, Vol. 317, No. 2000, p. 109-123, published online January 7, 2004, Wesselhoft, R. et. al., Nature Communications, Vol. 9, No. 2629, p. 1-10, July 6, 2018, and Goldberg, M. and Carmona, E., US 2018/0169146 A1, June 21, 2018. The rejection of Claim 11 are evidenced by England Biolabs, “A typical DNase I Reaction (M0303) V.1”, published January 17, 2015. The rejection of Claim 11 is evidenced by New England Biolabs 2, “Protocol for XRN-1 NEB M0338”, published January 2017.
Regarding Claim 13, Moore teaches a method which (a) provides a RNA having a 5’ and 3’ end and DNA that has a first region that hybridizes to the 5’ end and a second region that hybridizes to the 3’ end of the RNA molecule: “RNA and … cDNA bridge spanning the ends of the RNA. Hybridize by heating at 75 ° for 2 min” (p. 119, Procedure 2). Moore teaches (b) ligating the 5’ end of the linear RNA to the 3’ end of the linear RNA to create a product comprising of circular RNA, linear RNA, and linear DNA and (c) reacting the product with DNase (p. 119, Procedure 2, Ligation). Moore teaches DNase treatment removes the intermediate product: “Incubation with RNase-free DNase after the ligation reaction degrades the bridging eDNA template” (p. 123, DNase Treatment).
Moore does not teach DNase I and (d) where the product of the digested mixture of step (c) is reacted with an exonuclease.
Wesselhoft teaches a method where (b) products of a splint ligation reaction, comprising of circular polyribonucleotides, linear ribonucleotides, and linear polydeoxyribonucleotides, are (c) reacted with DNase I for 20 minutes wherein the second digestion mixture comprises an enriched population of circular polyribonucleotides (p. 8-9, circRNA design and purification).
Goldberg teaches a method where (b) products of a splint ligation reaction to create circular polyribonucleotides are (d) treated with an exonuclease including Xrn-1 and Exonuclease T for greater product purity: “non-circularized nucleic acid molecules may be digested with an RNase, e.g.,… Exonuclease T, … or XRN-1” (p. 2, [0022]); “XRN-1 exonucleases result in the highest purity of circularized product” (p. 2, [0031]).
Regarding Claim 13, it would have been obvious to one skilled in the art before the effective filing date to have performed a simple combination with the teachings of Moore, Wesselhoft, and Goldberg to create the method of Claim 13 by adding the step of DNase treatment taught by Wesselhoft and adding the step of exonuclease treatment taught by Goldberg to the method of Moore to create a higher purity product. . Moore teaches steps (a) and (b), Wesselhoft teaches steps (b) and (c), and Goldberg teaches steps (b) and (d). Each step is performed sequentially, and therefore performs the same purpose when combined together. The results of each step are predictable because Moore, Wesselhoft, and Goldberg were able to create an enriched population of circular RNA. One would be motivated to combine the step of DNase I as taught by Wesselhoft because Moore already teaches the use of DNase to remove unwanted DNA (p. 123, DNase Treatment).. One would be motivated to combine the step of exonuclease digestion because Goldberg teaches it removes unwanted linear RNA (p. 2, [0031]). Therefore, Claim 13 is obvious over Moore, Wesselhoft, and Goldberg.
Regarding Claim 14, Claim 14 is rejected under 35 USC 112(b) for failing to identify the limitations of U/μg. For compact prosecution, U/μg is interpreted as units of DNase I/ μg of RNA. Wesselhoft teaches a method using 0.2 units of DNase I per 1 μg of RNA 1 as evidenced by New England Biolabs (Steps 1 and 2), which is within 0.1 and 1 as described above for Claim 2. Therefore, Claim 14 is obvious over Moore, Wesselhoft, and Goldberg.
Regarding Claim 15, Wesselhoft teaches a method where step (c) is performed for 20 minutes at 37°C, which is at least 10 minutes as evidenced by New England Biolabs (Step 4) as described above for Claim 3. Therefore, Claim 15 is obvious over Moore, Wesselhoft, and Goldberg.
Regarding Claim 17, 18 and 19, Goldberg teaches a method using a 5’-phosphate dependent exonuclease, Xrn-1 (p. 2, [0022]). Therefore, Claims 17, 18, and 19 are obvious over Moore, Wesselhoft, and Goldberg.
Regarding Claim 21 and 22, Goldberg teaches a method using a 3’ exonuclease, Exonuclease T (p. 2, [0022]). Therefore, Claims 21 and 22 are obvious over Moore, Wesselhoft, and Goldberg.
Regarding Claim 23, Goldberg teaches a method where the digestion of step (d) is performed for at least 1 hour at 37 °C as evidenced by New England Biolabs 2 as described above for Claim 11 (Step 3). Therefore, Claim 23 is obvious over Moore, Wesselhoft, and Goldberg.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Krishna Nuggehalli Ravindra whose telephone number is (571)272-2758. The examiner can normally be reached M-Th, alternate F, 8a-5p est.
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/K.N.R./ Examiner, Art Unit 1636
/NEIL P HAMMELL/ Supervisory Patent Examiner, Art Unit 1636
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