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
Election/Restrictions
Applicant's election with traverse of groups I and II in the reply filed on 05/27/2025 is acknowledged.
Election of the following species on the reply filed on 05/27/2025 is acknowledged: The elected species are as follows:
1-methoxyethyl-6-(p-n-octylanilino)uracil for the small molecule inhibitor of UDG (Claim 1).
A Cas domain for a DNA-binding domain.
A Cas12a domain for a Cas domain
An activation-induced deaminase (AID) domain for a deaminase domain.
Not-fused for a structural relationship between fusion protein and npUGI.
The requirement was deemed proper and made FINAL in the action filed 09/24/2025.
Priority
The present application is a 35 U.S.C. 371 national stage filing of International Application No. PCT/US2020/058186, filed 10/30/2020.
Applicant’s claim for the benefit of a prior-filed parent provisional application 62/929007, filed on 10/31/2019 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged.
Thus, the earliest possible priority for the instant application is 10/31/2019.
Claims Status
Claims 8, 15-16, 20, 23, 26, 35, 37, 39, and 40 have been withdrawn from consideration as being drawn to non-elected subject matter, and claims 1-3, 5, 11, 14, 18, 21-22, 24-25, 28-30, 36, 38, and 43 have been considered on the merits. All arguments have been considered.
Withdrawn Objections & Rejections
Applicant's response filed 01/23/2026 has been considered. Rejections and/or objections not reiterated from the previous Office action mailed 09/24/2025 are hereby withdrawn.
The objections and rejections presented herein represent the full set of objections and rejections currently pending in the application.
Claim Rejections - 35 USC § 112(a) (Maintained)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 5 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The rejection is essentially identical to the rejection in the action recited in the action filed 09/24/2025, however is modified to address the amendments to the claims.
Regarding claim 5:
Claim interpretation
The claim recites “Cas12a domain comprises an amino acid sequence with at least 95% sequence identity” and recites ~62 Seq ID Nos. Seq ID NO: 350 will be used as an exemplary sequence. The following analysis extends to the additional Seq ID Nos encompassed by the instant claim.
Seq ID NO: 350 is an amino acid sequence comprising 1300 residues. The broadest reasonable interpretation of the claim limitation “at least 95% sequence identity” is an amino acid sequence that can differ from Seq ID NO: 350 by up to 5% (about 65 aa residues) compared to Seq ID NO: 350.
Each amino acid residue can be replaced by any other amino acid residue, thus there are 19 possible a replacements at up to 65 positions. This represents 2065 variants for a single 1300 residue polypeptide with variations at 65 residues. The claimed polypeptide, however, can have substitutions at any of the 1300 positions, and there are ~60 sequences which can comprise similar variations. Thus the claimed genus is very broad and comprises an extremely large number of molecules.
Teachings of the instant specification
The instant specification provides guidance as to the composition of the amino acid substitutions of the claimed Cas protein amino acid sequences.
The instant specification teaches Seq ID nos that the Cas12a domain can comprise (p3 0009). The instant specification also teaches the Cas12a domain can be a nickase domain or a catalytically dead dCas12a domain (p32 0035). The instant specification provides a section describing general Cas12a domains and teaches Cas12a is also known as Cpf1 (p72 0081-0084). The instant specification also describes some general parameters for amino acid substitutes/mutations in terms of number of residues mutated (p74-75). The instant specification teaches some specific single and double residue mutations of Cas12a (p75 0085-0086). The instant specification teaches unstructured regions predicted withing the Cas12a primary structure (p78 0087). The instant specification teaches bacterial species from which the Cas12a sequence can be derived (p80 0089) and that the Cas12a sequence can be codon-optimized (p81 0090). The instant specification teaches the disclosure can include the full-length Cas12a protein or a portion thereof (p82 0091) and that the Cas12a protein can be split (p82 para 0092).
The state of the art:
It is well known in the art that the effect of amino acid substitutions on protein activity is neither predictable nor well characterized for either Cas gene editing systems or for Cas proteins. A single amino acid substitution in the Cas9 protein can ablate nuclease activity that is required for gene editing (Kurihara et al (Nature Scientific Reports (2017)7:1013) (p10 para 7).
Tycko et all (Mol Cell(2016)63:3;1-31) teach a single point mutation of spCas9 can change activity from a nuclease into a nickase capable of cleaving only a single DNA strand (p8 para3).
This demonstrates that, while Cas variants are known in the art, the effect of changes to Cas protein amino acid sequences is highly specific to the specific residue(s) in question and small changes can have large effects on protein activity and function.
Thus, the effect of changes of up to 5% of the amino acid residues comprising a Cas variant as claimed must be experimentally tested using trial and error experimentation.
While Cas variants are known in the art, the species examples provided in the art are not of a large enough breadth to impart predictability on the genus as claimed.
Analysis
As described supra, the instant specification provides general guidance on Cas12a variants.
While the instant specification satisfies the written description requirement for Seq ID NO: 350-413, the species of Cas variants disclosed in the instant specification are not sufficient to predict the genus of Cas variants; “a sequence at least 95% identical to a sequence selected from SEQ ID NOs: 350-413”, as claimed, in view of the unpredictability of amino acid substitutions as evidenced by the art.
Alberts et al (Molecular Biology of the Cell. 4th edition. New York: Garland Science;2002) teach that each of the 20 amino acids is chemically distinct and only a very small fraction of the vast set of conceivable polypeptide chains would adopt a single, stable three-dimensional conformation (p7 para 2-3). In the case of substitution of residues in a functional protein for which function requires a specific structure, the effect of amino acid changes would have to be assessed by trial-and-error to determine the effect of specific residue changes.
Tycko teach even a single point mutation of a Cas protein can change activity of the protein. One of ordinary skill in the art would understand that Cas protein function requires binding to nucleic acid sequences, and often protein complexes, for a functional system. One of ordinary skill in the art would also understand that the effect of amino acid substitutions in the Cas sequence can have unpredictable effects on the encoded protein structure and thus binding activity and function.
Furthermore, the instant specification provides no guidance as how to avoid losing key structural, binding, or enzymatic activity of Cas proteins with amino acid substitution of up to 65 residues and the art does not provide a remedy.
Claim Rejections - 35 USC § 103 (Maintained)
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.
Claims 1- 3, 5, 11, 14, 18, 21-22, 24-25, 28-30, 36, 38, and 43 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al (US 2019/0312828 A1; as cited in the IDS filed on 12/21/2022) in view of Suksangpleng et al (Malaria Journal (2014)13(1-15) as cited in the IDS filed on 12/21/2022), Zhang et al (US 9,790,490 B2), Sekino et al (JBC(2000)275:47;1-5), and as evidenced by Strelow et al (Mechanism of Action Assays for Enzymes. 2012 May 1 Eli Lilly & Company and the National Center for Advancing Translational Sciences; Retrieved from the Internet: https://www.ncbi.nlm.nih.gov/books/NBK92001/).
Regarding claim 1, 21, 22, 24, 25: Liu teach targeted editing of nucleic acids, including editing a single site withing the genome (abstract). Liu teach a fusion protein comprising a DNA binding-protein, a cytidine deaminase domain, and a uracil glycosylase inhibitor (claim 1).
Liu do not teach the uracil glycosylase inhibitor (UGI) is a non-protein uracil-DNA glycosylase inhibitor that is the small molecule 1-methoxyethyl-6-(p-n-octylanilino)uracil.
Suksangpleng teach non-protein uracil-derived compounds that are UDG inhibitors (npUGI) (p1 col1 para4). Suksangpleng test 12 uracil-derived compounds for effect on glycosylase enzyme activity and determine cytotoxicity of the compounds (p1 col2 para1). Suksangpleng teach 1-methoxyethyl-6-(p-n-octylanilino)uracil inhibits uracil-DNA glycosylase to the greatest extent compared to the other compounds tested, and exhibits low cytotoxicity (p12 col1 para2, Table 5).
It would have been prima facie obvious to substitute the UGI taught by Liu for the UGI taught by Suksangpleng because the UGI taught by Suksangpleng exhibits robust inhibition activity and low cytotoxicity. Furthermore, one of ordinary skill in the art would understand the concentration of small molecule inhibitors can be precisely modulated independent of fusion protein expression, resulting in a more flexible base editing system, and the results would have been predictable.
Substitution of one element for another known in the field, wherein the result of the substitution would have been predictable, is considered to be obvious. See KSR International
Regarding claims 2, 3, 5: The teachings of Liu are discussed supra. Liu also teach the DNA binding protein is Cas12a (Cpf1) (claim 1). Liu do not disclose the amino acid sequence of the Cas12a DNA binding domain.
Zhang et al (US 9,790,490 B2) teach sequence 1110, which has 100% sequence identity with seq ID 350 of the instant claim.
It would have been prima facie obvious to substitute the Cas12a domain in the fusion protein taught by Liu with the Cas12a sequence taught by Zhang because both inventions are drawn to a Cas12a protein. There would have been a reasonable expectation that the Cas12a protein of Zhang would work equivalently to the Cas12a protein disclosed by Liu because both systems utilize the Cas12a variant in their gene editing systems, and the results would have been predictable.
Substitution of one element for another known in the field, wherein the result of the substitution would have been predictable, is considered to be obvious. See KSR International Co. v Teleflex Inc 82 USPQ2d 1385 (US 2007) at page 1395.
Regarding claim 11: The teachings of Liu are discussed above. Liu also teach the guide RNA target sequence comprises a nucleotide sequence that complements a target site, which mediates binding of the nuclease/RNA complex to said target site, providing the sequence specificity of the nuclease:RNA complex (p18 0212). Liu further teach the guide RNA is from 15-100 nucleotides long and comprises a sequence of at least 10 contiguous nucleotides that is complementary to target sequence (p65 0398, claim 42).
Regarding claims 14 and 18: The teachings of Liu are discussed above. Liu also teach the cytidine deaminase domain is an APOBEC family activation-induced deaminase (AID) domain (p153 0826, Fig136B).
Regarding claim 28: The teachings of Liu and Suksangpleng are discussed supra. Neither Liu nor Suksangpleng explicitly teach the compound of formula I is incorporated into a macromolecule or into an oligonucleotide.
Strelow teach there are three types of enzyme inhibition by small molecules (competitive, noncompetitive and uncompetitive) and that all three mechanisms require binding of the small molecule inhibitor to the enzyme (p2/3 types of inhibition).
Thus, while Liu and Suksangpleng do not explicitly teach incorporation of the compound of formula I into a macromolecule, the compound of formula I is shown to inhibit uracil-DNA glycosylase and thus must bind the enzyme. Binding the enzyme reads on “incorporation into a macromolecule”.
Regarding claim 29: The teachings of Liu and Suksangpleng are discussed supra. Neither Liu nor Suksangpleng explicitly teach the compound of formula I is incorporated into an oligonucleotide.
Sekino teach altering the UDG substrate using synthetic substrate analogs that the bind the enzyme but cannot be processed is an approach to trap an enzyme-substrate interaction (p2 col2 para1). Sekino teach uracil analogs are synthesized and incorporated into 25mer oligonucleotides using standard solid phase chemistry (p3 col1 para 5).
Regarding claim 30: The teachings of Liu and Suksangpleng are discussed above. Liu also teach editing a single site within the genome of a subject (abstract), wherein the subject can human, or a non-human animal such as a rodent, fish, fly, or nematode (p27 para0234).
Regarding claim 36: The teachings of Liu and Suksangpleng are described supra. Suksanpleng do not teach that the npUGI is chemically linked.
It would have been prima facie obvious to substitute the npUGI of Suksangpleng into the gene editing system of Liu et al because the gene editing system of Liu requires a UGI, and Suksangpleng discloses the compound of formula 1 is not toxic to mammalian cells and inhibits UDG (abstract).
There would have been a reasonable expectation that the npUGI would have functioned equivalently in the gene editing system taught by Liu, and the results would have been predictable.
Substitution of one element for another known in the field, wherein the result of the substitution would have been predictable, is considered to be obvious. See KSR International Co. v Teleflex Inc 82 USPQ2d 1385 (US 2007) at page 1395.
Regarding claim 38: The teachings of Liu are described supra. Liu also teach that the Cas12a (Cpf1) is a nickase (p154 0846).
Regarding claim 43: The teachings of Liu are discussed supra. Liu also teach editing a target nucleic acid molecule by contacting a target nucleic acid molecule with the base-editing system (claim 164).
Response to Arguments
The responses are directed to the Arguments filed 01/23/2026, all arguments have been considered.
Regarding Arguments directed to 35 USC § 112(a):
Specifically, the claim has been amended to recite “95% sequence identity”. The rejection is essentially maintained, with changes to reflect the claim amendments.
Regarding Arguments directed to 35 USC § 103:
Applicant asserts one of ordinary skill in the art would not have been
motivated to substitute the UGI of Liu with any non-protein UGI, let alone the small molecule UGI of Suksangpleng, to arrive at the pending claims.
In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007).
MPEP 2144.06 reads “In order to rely on equivalence as a rationale supporting an obviousness rejection, the equivalency must be recognized in the prior art, and cannot be based on applicant’s disclosure or the mere fact that the components at issue are functional or mechanical equivalents. In re Ruff, 256 F.2d 590, 118 USPQ 340 (CCPA 1958)”.
In this case, both teachings disclose a UGI to perform the same function, one UGI is a protein and one UGI is a small molecule. It is reasonable to conclude one of ordinary skill in the art would understand that a small molecule could substitute for an amino acid molecule in performing a function when both molecules are known in the art to perform the same function.
The rejection is maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ANDREA LYNNE MORRIS SPENCER whose telephone number is (571)272-3328. The examiner can normally be reached Monday-Friday 9:00-5:00.
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/ANDREA LYNNE MORRIS SPENCER/Examiner, Art Unit 1631
/TAEYOON KIM/Primary Examiner, Art Unit 1631
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