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
Claims 2-13, 15, 17, 40, and 41 are cancelled. Claim 42 has been newly added. Claims 1, 14, 16, 18-39 and 42 are pending. Claims 33-39 are withdrawn. Claims 1, 14, 16, 18-32 and 42 are under examination.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10/20/2025 has been entered.
Response to Arguments
With respect to the rejection of claims 1, 14, 16, and 18-32 under 35 USC 103, Applicant's arguments filed 10/20/2025 have been fully considered but they are not persuasive. Applicant’s arguments are in view of the claim amendments filed 10/20/2025. Applicant argues that none of the previously cited references teach an RNA recognition domain with 10 recognition units connected in series to form an RNA base recognition region, wherein each recognition unit recognizes an RNA base, wherein each recognition unit is an α-helix repeated sequence containing three amino acids at a specific position responsible for binding RNA bases, wherein the side chain amino acids at positions 12 and 16 of the α-helix repeated sequence bind to RNA bases through hydrogen bonds, while the amino acid at position 13 of the α-helix repeated sequence serves as an auxiliary binding, wherein different combinations at positions 12 and 16 of the α-helix repeated sequence are as follows:
a pairing combination of SQ or CQ recognizes A as the RNA base;
a pairing combination of NQ recognizes U as the RNA base;
a pairing combination of SE recognizes G as the RNA base; and
a pairing combination of SR recognizes C as the RNA base.
However, the amended claims are unclear as to what the claim requires. The claims recite amino acid positions 12, 13, and 16 but does not recite a reference sequence identified by a SEQ ID NO. Therefore, it is unclear what the sequence of the RNA recognition domain is. Moreover, it is unclear if the claim requires a recognition unit with each of the recited pairing combinations, or if the claim is simply reciting what bases would be recognized if the recited pairing combinations were employed. Therefore, it is unclear what sequence residues 12 and 16 are part of, and it is unclear what those residues should be. Under BRI, any RNA recognition domain containing 10 recognition units meets the limitations of the instant claims, therefore, the 103 rejection is maintained.
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 1, 14, 16, and 18-32 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.
Claim 1 recites: wherein the RNA recognition domain contains 10 recognition units connected in series to form an RNA base recognition region, wherein each recognition unit recognizes an RNA base, wherein each recognition unit is an α-helix repeated sequence containing three amino acids at a specific position responsible for binding RNA bases, wherein the side chain amino acids at positions 12 and 16 of the α-helix repeated sequence bind to RNA bases through hydrogen bonds, while the amino acid at position 13 of the α-helix repeated sequence serves as an auxiliary binding, wherein different combinations at positions 12 and 16 of the α-helix repeated sequence are as follows:
a pairing combination of SQ or CQ recognizes A as the RNA base;
a pairing combination of NQ recognizes U as the RNA base;
a pairing combination of SE recognizes G as the RNA base; and
a pairing combination of SR recognizes C as the RNA base…
The recitation of amino acids at specific positions without a reference sequence identified by a SEQ ID NO is considered indefinite. It is unclear what the sequence of the RNA base recognition unit is. It is unclear what amino acids are at residues 12 and 16, i.e., it is unclear if the claim requires an RNA base recognition unit with each of the recited pairing combinations. Therefore, one of ordinary skill in the art would not know what is required by the claim.
Claims 14, 16, and 18-32 are also rejected as they depend from claim 1.
Claim Rejections - 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.
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.
Under BRI, in is interpreted that an RNA recognition domain with 10 recognition units meets the limitations of the instant claim.
Claims 1, 14, 18-22, 25-30, and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Rosbash et al., (WO 2018/017144 A1), previously cited, in view of Zhao et al., 02/27/2018 (Expanding RNA binding specificity and affinity of engineered PUF domains), previously cited, as evidenced by Abassi et al., 2011 (Pumilio Puf domain RNA-binding proteins in Arabidopsis), previously cited.
Regarding claim 1, Rosbash teaches a fusion polypeptide comprising an RNA binding polypeptide, i.e., an RNA recognition domain, operably linked to an RNA modifying enzyme, i.e., a utility domain (e.g., adenosine deaminase, cytidine deaminase) (Page 1, lines 20-23).
Rosbash does not teach that the RNA binding/recognition domain comprises a PUF domain with 10 recognition units.
However, Zhao teaches a PUF domain with 10 repeats, i.e., 10 recognition units (Page 4772, Column 1, Materials and Methods). Zhao teaches that the engineered PUFs would in principle recognize the cognate RNA targets containing 10 bases (Page 4774, Column 1, Paragraph 1), i.e., each recognition unit recognizes an RNA base.
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to substitute the PUF domain with 10 recognition units taught by Zhao for the PUF domain in the RNA binding/recognition domain taught by Rosbash. One of ordinary skill in the art would have been motivated to do so because Zhao teaches that the engineered PUFs bind to their RNA targets specifically and PUFs with more repeats have higher binding affinity that the canonical eight-repeat domains, with a binding affinity peak of those with 9 and 10 repeats (Abstract). One of ordinary skill in the art would have had a reasonable expectation of success because substituting protein domains for those of similar function is well within the knowledge of one of ordinary skill, and the results are reasonably predictable.
Regarding claim 14, Rosbash teaches that the RNA modifying enzyme is the catalytic domain of the Drosophila homolog of Adenosine Deaminases Acting on RNA (ADAR) (Page 4, line 28).
Regarding claim 18, Rosbash teaches that the fusion polypeptide further contains a sequence tag (Page 3, lines 30-31).
Regarding claim 19, Rosbash teaches that the RNA binding proteins can be fused to an RNA modifying enzyme to form an RNA binding protein-RNA modifying enzyme fusion polypeptide (Page 38, lines 5-7). Rosbash specifically teaches a fusion polypeptide in which the RNA binding protein, Thor, is linked via a spatial linker region to the RNA modifying enzyme, ADAR (Page 50, lines 7-20). Therefore, the fusion polypeptide of Rosbash is represented by instant Formula III.
Regarding claim 20, Rosbash teaches a fusion polypeptide in the order of Thor-ADAR (Page 50, lines 15-21), i.e., at the Thor RNA binding protein is located at the N-terminus of the ADAR RNA modifying enzyme.
Regarding claims 21 and 22, as stated above, Rosbash teaches that the RNA modifying enzyme is the catalytic domain of the Drosophila homolog of Adenosine Deaminases Acting on RNA (ADAR) (Page 4, line 28).
Regarding claim 25 and 26, Rosbash teaches the use of seven characterized cytidine deaminases, including APOBEC, and teaches the use of mouse APOBEC1 (Page 57, lines 8-9).
Regarding claim 27, Rosbash also teaches the use of human APOBEC3A (Page 59, line 27).
Regarding claim 28, as stated, Zhao teaches that the engineered PUFs would in principle recognize the cognate RNA targets containing 10 bases (Page 4774, Column 1, Paragraph 1)
Regarding claim 29, although Zhao does not specifically disclose that the PUF domain recognizes a gene transcript, it is well-known that a main function of PUF domains is to regulate mRNA processing. For example, PUF proteins are involved in translational repression of transcripts through direct binding to mRNA, as evidenced by Abassi et al., 2011 (Abstract). Therefore, it is interpreted that recognition of a gene transcript is an inherent characteristic of the PUF domain taught by Zhao.
Regarding claim 30, as stated above, Rosbash teaches an RNA editing enzyme comprising an RNA modifying enzyme linked to an RNA recognition domain, while Zhao teaches a PUF domain with 10 repeats, i.e., 10 recognition units (Page 4772, Column 1, Materials and Methods). Zhao teaches that the engineered PUFs would in principle recognize the cognate RNA targets containing 10 bases (Page 4774, Column 1, Paragraph 1), i.e., each recognition unit recognizes an RNA base. Zhao also teaches that PUFs with more repeats will minimize the off-target effect (Page 4772, Column 1, Paragraph 2). Therefore, reduction of the off-targeting rate by 10-fold would be an inherent characteristic of an RNA-editing enzyme comprising the PUF domain taught by Zhao.
Regarding claim 32, as stated above, Rosbash teaches that the RNA modifying enzyme is the catalytic domain of the Drosophila homolog of Adenosine Deaminases Acting on RNA (ADAR) (Page 4, line 28)
Claims 16 and 31 are rejected under 35 U.S.C. 103 as being unpatentable over Robash et al., (WO 2018/017144 A1) and Zhao et al., 2018 (Expanding RNA binding specificity and affinity of engineered PUF domains) as applied to claim 1 above, and further in view of Wang et al., (US 11,434,484 B2), previously cited.
Robash teaches a fusion protein comprising an RNA recognition/binding domain and an RNA editing/utility domain, while Zhoa teaches an RNA recognition PUF domain with 10 recognition units.
The combination of Robash and Zhao does not teach an RNA editing enzyme comprising RNA methylase, RNA demethylase, or pseudouridine synthase.
However, regarding claim 16, Wang teaches a DNA or RNA editing enzyme complex comprising a fusion polypeptide comprising PUF domains (Column 1, line 61; Column 2, lines 5-18). Wang teaches that a fusion partner may be linked to the PUF domain, and that the fusion partner may exhibit enzymatic activity, and may include polypeptides that provide for demethylase activity (Column 40, lines 19-22).
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to add an enzyme with RNA demethylase activity, as taught by Wang, to the RNA editing domain of the fusion taught by Robash, with a PUF domain containing 10 recognition units, as taught by Zhao. One of ordinary skill in the art would have been motivated to do so because Wang teaches that enzymes with demethylase activity are suitable fusion partners for fusion proteins comprising PUF domains (Column 40, lines 19-22). One of ordinary skill in the art would have had a reasonable expectation of success because Robash, Zhao, and Wang are in the same field of endeavor of RNA editing enzyme development.
Regarding claim 31, Wang teaches a PUF domain sequence, SEQ ID NO:4, with 100% sequence identity to instant SEQ ID NO:1 (alignment in previous office action on 7/18/2025).
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Rosbash et al., (WO 2018/017144 A1), and Zhao et al., 02/27/2018 (Expanding RNA binding specificity and affinity of engineered PUF domains), as applied to claim 21 above, and further in view of UniProt ID Q59EC0_HUMAN, integrated into UniProt 04/26/2005.
See discussion of Robash and Zhao, which is incorporated into this rejection as well.
The combination of Robash and Zhao do not teach the sequence of the effector domain of human ADAR1.
However, UniProt ID Q59EC0_HUMAN teaches a sequence with 100% sequence identity to instant SEQ ID NO:2 (see alignment attached to this Office action).
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to substitute the ADAR1 sequence taught by UniProt ID Q59EC0_HUMAN for the RNA editing enzyme taught by modified Robash. One of ordinary skill in the art would have been motivated to do so because Rosbash teaches that the catalytic domain, i.e., the effector domain, of the RNA modifying enzyme may be human ADAR1 (Page 4, lines 30-31), while UniProt ID Q59EC0_HUMAN teaches that the region encompassing instant SEQ ID NO:2 is the editase, i.e., the catalytic or effector domain, of human ADAR1 (Family and Domains). One of ordinary skill in the art would have had a reasonable expectation of success because replacing domains for those of similar function is well-known to those of ordinary skill and the results are reasonably predictable.
Claim 24 is rejected under 35 U.S.C. 103 as being unpatentable over Rosbash et al., (WO 2018/017144 A1), and Zhao et al., 02/27/2018 (Expanding RNA binding specificity and affinity of engineered PUF domains), as applied to claim 21 above, and further in view of UniProt ID RED1_HUMAN, integrated into UniProt 11/01/1997.
See discussion of Robash and Zhao, which is incorporated into this rejection as well.
The combination of Robash and Zhao do not teach the sequence of the effector domain of human ADAR2.
However, UniProt ID RED1_HUMAN teaches a sequence with 100% sequence identity to instant SEQ ID NO:3 (see alignment attached to this Office action).
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to substitute the ADAR2 sequence taught by UniProt ID RED1_HUMAN for the RNA editing enzyme taught by modified Robash. One of ordinary skill in the art would have been motivated to do so because Rosbash teaches that the catalytic domain, i.e., the effector domain the RNA modifying enzyme may be human ADAR2 (Page 4, lines 30-31), while UniProt ID RED1_HUMAN teaches that the region encompassing instant SEQ ID NO:3, is the editase, i.e., the catalytic or effector domain, of human ADAR2 (Family and Domains). One of ordinary skill in the art would have had a reasonable expectation of success because replacing domains for those of similar function is well-known to those of ordinary skill and the results are reasonably predictable.
Claim 42 is rejected under 35 U.S.C. 103 as being unpatentable over Rosbash et al., (WO 2018/017144 A1), previously cited, in view of Zhao et al., 02/27/2018 (Expanding RNA binding specificity and affinity of engineered PUF domains), previously cited, and Bryson et al., (WO 2019/217943 A1), with an effective filing date of 05/11/2018.
Rosbash teaches a fusion polypeptide comprising an RNA binding polypeptide, i.e., an RNA recognition domain, operably linked to an RNA modifying enzyme, i.e., a utility domain (e.g., adenosine deaminase, cytidine deaminase) (Page 1, lines 20-23). Rosbash specifically teaches a fusion polypeptide in which the RNA binding protein, Thor, is linked via a spatial linker region to the RNA modifying enzyme, ADAR (Page 50, lines 7-20)
Rosbash does not teach that the RNA binding/recognition domain comprises a PUF domain with 10 recognition units, and Linker2, Linker7, XTEN, Linker20, or Linker40.
Zhao teaches a PUF domain with 10 repeats, i.e., 10 recognition units (Page 4772, Column 1, Materials and Methods). Zhao teaches that the engineered PUFs would in principle recognize the cognate RNA targets containing 10 bases (Page 4774, Column 1, Paragraph 1), i.e., each recognition unit recognizes an RNA base.
Zhao does not teach the use of Linker2, Linker7, XTEN, Linker20, or Linker40.
However, Bryson teaches an RNA binding domain-RNA nuclease fusion protein that may be linked via the XTEN linker (para. [0106]).
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to substitute the PUF domain with 10 recognition units taught by Zhao for the PUF domain in the RNA binding/recognition domain taught by Rosbash, and to substitute the XTEN linker as taught by Bryson for the linker of Robash. One of ordinary skill in the art would have had a reasonable expectation of success because substituting protein domains and linkers for those of similar function is well within the knowledge of one of ordinary skill, and the results are reasonably predictable. Robash, Zhao, and Bryson are also in the same field of endeavor of RNA editing enzyme development.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RACHEL EMILY MARTIN whose telephone number is (703)756-1416. The examiner can normally be reached M-Th 8:30-16:00, F 8:30-10:00 EST.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/RACHEL EMILY MARTIN/Examiner, Art Unit 1657