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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 24 March 2026 has been entered.
DETAILED ACTION
Applicant’s amendment filed on 24 March 2026 is entered. Claims 2 and 17 are amended.
Claims 1-4, 7, 9-11, 17, 19-20, 22-23, 26, and 28-29 are pending. Claims 10, 26, and 28-29 remain withdrawn. Claims 1-4, 7, 9, 11, 17, 19-20, and 22-23 are examined.
Claim Rejections - 35 USC § 112
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.
Claims 1-4, 7, 11, 17, 19-20, and 23 are 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(s) 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.
Claim 2 recites the limitation “…an amino acid sequence of SEQ ID NO: 2 or a functionally equivalent variant thereof having at least 80% sequence identity to SEQ ID NO: 2”. Claim 3 recites “wherein the catalytic domain of a thermophile TDG has an amino acid sequence that is at least 90% identical to SEQ ID NO: 3”. Claim 7 recites the hybrid glycosylase polypeptide comprises an amino acid sequence at least 90% identical to SEQ ID NO: 1. Claim 17 recites the limitations “…an amino acid sequence of SEQ ID NO: 2 or a functional equivalent variant thereof having at least 80% sequence identity to SEQ ID NO: 2…” and “…a substitution of Y126K corresponding to SEQ ID NO: 3 or a functionally equivalent variant thereof having at least 80% sequence identity to SEQ ID NO: 3.” Claim 23 recites a hybrid lyase polypeptide comprising an amino acid sequence that is at least 90% identical to SEQ ID NO:189 wherein amino acid 155 is a lysine.
Multiple genera exist within the claims that lack sufficient written description: (a) the genus of polypeptides comprising a human activator segment with an amino acid sequence with at least 80% identity to SEQ ID NO: 2; (b) the genus of polypeptides comprising a catalytic domain of a thermophile TDG with an amino acid sequence with at least 90% identity to SEQ ID NO: 3; (c) the genus of polypeptides comprising “functionally equivalent variants” of human activator segments and/or catalytic domains of thermophile TDGs; (d) the genus of polypeptides comprising amino acid sequences with at least 90% identity to SEQ ID NO: 1.
The term “a functionally equivalent variant thereof” is a broad term. Although the claims partially limit the size of the genus to being those based off of a particular structure (those of SEQ ID NOs: 2 and/or 3), the scope of the claim term “functionally equivalent variant” is still substantially large as it would encompass various substitutions, deletions, and additions to the base sequences SEQ ID NOs: 2 and 3. Turning to the specification, there is no clear and explicit special definition of the claim term “functionally equivalent variant”. There are locations within the specification that provide some guidance on what is meant by the term “variant”, including some guidance stating that the variants retain the same functions as the polypeptides they are based on (see specification [0011], [0012], [0023], [0024], [0079], and [0083] discussed further below), but this guidance does not provide adequate description that supports what variations (changes to structure) can be tolerated for the variants to retain the same functions as that of the polypeptides from which they are based (SEQ ID NOs: 2 and 3). Thus, the disclosure does not provide sufficient direction such that one of ordinary skill in the art can visualize which species of the genus of functionally equivalent variants would exhibit the functional requirements such to convey that Applicant had sufficient possession of the entire genus of “functionally equivalent variants thereof”. This means that, because of the lack of guidance on what specific variations and changes to structure of the variants preserve the functions of their progenitors, the genus of variants claimed is sufficiently broad such that any amino acid sequence with 80% identity to SEQ ID NO:2 and any amino acid sequence with 80% identity to SEQ ID NO:3 is encompassed within the claimed genera of functionally equivalent variants. This lack of guidance is also extended to the other genera which lack sufficient written description: the genus of polypeptides comprising a catalytic domain of a thermophile TDG with an amino acid sequence with at least 90% identity to SEQ ID NO: 3 and the genus of polypeptides comprising amino acid sequences with at least 90% identity to SEQ ID NO: 1.
The guidance on the claim term “functionally equivalent variant” within the specification paragraphs cited above is sufficiently broad such that it can encompass variant sequences that are completely different in sequence and/or structure from their base starting sequences. Paragraphs [0011] and [0023] of the specification state that the variant of the amino terminal human activator segment (which corresponds to SEQ ID NO: 2) can have 1-10 amino acid substitutions, deletions, and/or additions while maintaining the progenitor polypeptide’s function. However, the last sentences of paragraphs [0011] and [0023] also state that the variant sequences can have one or more amino acid substitutions, deletions, or additions, but these last sentences do not state that any particular structure must be retained. Likewise, paragraphs [0012] and [0024] state that the variant of the catalytic segment (which corresponds to SEQ ID NO: 3) can be at least 60% identical to 200-221 consecutive amino acids of SEQ ID NO: 3. The paragraphs go on to state that the variant of the catalytic segment can have 1-10 amino acid substitutions, deletions, and/or additions while maintaining the progenitor polypeptide’s function. However, the last sentences of paragraphs [0012] and [0024] also state that the variant sequences can have one or more amino acid substitutions, deletions, or additions, but these last sentences do not state that any particular structure must be conserved. Paragraph [0079] of the specification provides some basic guidance on substitution, insertion, and deletion variants, including conservative amino acid substitutions and/or non-conservative amino acid substitutions, and also states that the polypeptide variants may possess an insertion (addition) of one or more residues, and that the variant hybrid sequence can form the appropriate structure and conformation for its enzymatic function, but paragraph [0079] fails to provide what specific variations or changes in structure can allow the variant hybrid polypeptide to form the appropriate conformation to preserve its enzymatic function. Paragraph [0083] states that amino acid sequence variants of polypeptides or polypeptide segments of the instant compositions can be substitutional, insertional (additional), or deletion variants, with modifications affecting 1-250 or more non-contiguous or contiguous amino acids of a polypeptide. In the context of the instant invention this means a “functionally equivalent variant” can have a different amino acid sequence than the amino acid sequence that the variant is based on, so long as it is 80% identical to sequences SEQ ID NOs: 2 or 3. Even though the genus of “variants” has been limited to “functionally equivalent variants thereof”, the claims and the specification paragraphs cited above do not provide sufficient description or indication of what substitutions, insertions, deletions, and/or additions could be tolerated such that the variant polypeptide and/or protein could maintain its function.
Additionally, the variants are also not limited to being the same length as the amino acid sequence from which they are based because the specification describes the variants can include one or more insertions/additions without any limit to preserving any specific function, meaning the length of the variant amino acid sequences encompassed in the genus of “functionally equivalent variants” can theoretically be much longer than the SEQ ID NOs: 2 or 3 from which the functionally equivalent variants are based (specification [0011], [0012], [0023], and [0024]), especially in the absence of any sufficient guidance in the disclosure and in the art on what changes could be tolerated such that the variant polypeptide and/or protein could maintain its function. The number of possible permutations of sequences covered by the broad claimed genus of “functionally equivalent variants” is substantial. Applicant has not described a representative number of species of amino acid sequence members encompassed by the genus of “functionally equivalent variants” as claimed. Given that SEQ ID NO: 2 is 29 amino acids long, the number of possible ordered permutations with replacements is 5.36x1037 possible unique sequences (2029 = 5.36x1037). Likewise, given that SEQ ID NO: 3 is 221 amino acids long, the number of possible ordered permutations with replacements is 3.36x10287 possible unique sequences (20221 = 3.36x10287). The above calculations also do not take into account that neither the claims nor the specification limit the amino acids in the variant amino acid sequences to be natural amino acids. The broadest reasonable interpretation of an amino acid includes the 20 natural L-amino acids that natural proteins comprise, but also synthetic amino acids and D-amino acids. Including these other amino acid possibilities in the above number of permutations would result in an even larger genus of variants.
Thus, a sufficient number of species in the genera of (a) the genus of polypeptides comprising a human activator segment with an amino acid sequence with at least 80% identity to SEQ ID NO: 2; (b) the genus of polypeptides comprising a catalytic domain of a thermophile TDG with an amino acid sequence with at least 90% identity to SEQ ID NO: 3; (c) the genus of polypeptides comprising “functionally equivalent variants” of human activator segments and/or catalytic domains of thermophile TDGs; (d) the genus of polypeptides comprising amino acid sequences with at least 90% identity to SEQ ID NO: 1 is not described in Applicant’s disclosure such to convey that Applicant had sufficient possession of the entire genera.
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 1-4, 7, 9, 11, 17, 19-20, and 22 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 claims 1 and 17, claim 1 recites a hybrid glycosylase polypeptide comprising an amino terminal human thymine DNA glycosylase (TDG) activator segment linked to a catalytic domain of a thermophile TDG, and claim 17 recites a hybrid polypeptide comprising an amino terminal human thymine DNA glycosylase (TDG) activator segment…linked to a catalytic domain of a thermophile TDG. It is unclear if the term “amino terminal” is limiting (1) the position of the human TDG activator segment in the whole hybrid polypeptide (i.e. the activator segment is the amino terminal end of the hybrid polypeptide); or (2) the position of the activator segment within a human TDG (i.e. the activator segment is the amino terminal end of a human TDG).
Regarding claims 2 and 17, claims 2 and 17 recite the human activator segment has an amino acid sequence of SEQ ID NO: 2 or a functionally equivalent variant thereof, and claim 17 further recites the catalytic domain of a thermophile TDG…or a functionally equivalent variant thereof. It is not clear if the limitation “a functionally equivalent variant” means: (1) that the variant sequences have the same (equivalent) overall functions as the parent activator segment of SEQ ID NO: 2 or catalytic domain of a thermophile TDG of SEQ ID NO: 3, but are not required to have the exact same (or equivalent) levels or enzymatic activities as those of SEQ ID NOs: 2 or 3; or (2) that the variant sequences must have equivalent functional capabilities such that they perform to the exact same (or equivalent) level or enzymatic activities as the parent activator segment of SEQ ID NO: 2 or catalytic domain of a thermophile TDG of SEQ ID NO: 3. For example, it is unclear if the claimed “functionally equivalent variant” of the activator segment of SEQ ID NO: 2 may include a polypeptide that still activates the glycosylase, but does not activate it as much as or to the same extent as the activator segment of SEQ ID NO: 2.
Regarding claim 17, the claim recites the hybrid polypeptide comprises a catalytic domain of a thermophile TDG comprising a substitution of Y126K corresponding to SEQ ID NO: 3.
The claim does not limit the catalytic domain of the thermophile TDG to have an amino acid sequence of SEQ ID NO: 3; it merely limits the catalytic domain of a thermophile TDG to comprise the substitution Y126K corresponding to SEQ ID NO: 3. The sequence identifier SEQ ID NO: 3 limits the Y126K substitution's position in the catalytic domain of the thermophile TDG and the type of substitution (i.e. Y to K), but does not limit the TDG's sequence to be SEQ ID NO: 3. The broadest reasonable interpretation of the catalytic domain of the thermophile TDG includes sequences with varying lengths.
It is unclear if the Y126K substitution must occur at position 126 for every possible sequence within the "catalytic domain of a thermophile TDG" genus, even if position 126 of the thermophile TDG's sequence does not correspond to position 126 of SEQ ID NO: 3. For example, an example catalytic domain of a thermophile TDG (hereinafter Example A) has a sequence that has residue Y150, which aligns with residue Y126 of SEQ ID NO: 3. It is unclear if the claim requires Example A’s residue at position 126 to be substituted from Y to K, even though residue Y150 of Example A corresponds to position Y126 of SEQ ID NO: 3. It is also unclear that, if a variant TDG's sequence residue position 126 is not a Y, would the substitution to K be required, even though that position is not a Y.
Claims 2-4, 7, 9, and 11 are dependent on claim 1, and claims 19-20 and 22 are dependent on claim 17, so those dependent claims are indefinite for the same reasons.
It is suggested to amend claim 23 to recite:
A hybrid lyase polypeptide comprising the amino acid sequence of SEQ ID NO: 189, wherein amino acid 155 is substituted with a lysine.
It is also suggested to amend claim 1 to include the limitations of claim 9, such that claim 1 would recite:
A hybrid glycosylase polypeptide comprising an amino terminal human thymine DNA glycosylase (TDG) activator segment linked to a catalytic domain of a thermophile TDG, wherein the polypeptide has the amino acid sequence of SEQ ID NO:1.
It is also suggested to amend claim 17 to recite:
A hybrid polypeptide comprising an amino terminal human thymine DNA glycosylase (TDG) activator segment linked to a catalytic domain of a thermophile TDG, wherein the polypeptide has the amino acid sequence of SEQ ID NO: 189.
Pertinent References
The following is a statement of the relevance of prior art not used in rejections but pertinent to the claims:
The closest prior art is Coey et al. (Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues, 10248–10258 Nucleic Acids Research, 2016, Vol. 44, No. 21) and Horst and Fritz (Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF, The EMBO Journal vol.15 no.19 pp.5459-5469, 1996).
Coey teaches an activator segment of a human TDG with a sequence identical to instant SEQ ID NO: 2. Horst teaches a thermophile TDG with a sequence identical to instant SEQ ID NO: 3. However, one of ordinary skill in the art would not have found it obvious to fuse the activator segment of Coey’s human TDG to the N-terminus of Horst’s thermophile TDG.
Human TDG and thermophile TDG are fundamentally and structurally different TDGs that merely share the same functionality of excising thymine and uracil DNA mispairs. The sequences, 3D structures, and mechanisms of actions are fundamentally different.
The human TDG uses an alpha-beta fold catalytic center, whereas the thermophile TDG uses a Helix-hairpin-helix (HnH) catalytic center. The human activator segment is located directly adjacent to the alpha-beta fold catalytic center of the human TDG (Coey Fig. 3, and Human TDG Uniprot accession no. Q13569, https://www.uniprot.org/uniprotkb/Q13569, accessed 01 May 2026). If Coey’s human activator segment were to be fused to the N-terminal end of the thermophile TDG, as the 103 rejection stated, it would be on the physically opposite end of the 3D protein from the HnH catalytic center of the thermophile TDG (Thermophile TDG Uniprot accession no. P29588, https://www.uniprot.org/uniprotkb/P29588, accessed 01 May 2026, 3D structure with notable domains indicated below).
PNG
media_image1.png
498
432
media_image1.png
Greyscale
The human activator segment taught by Coey non-selectively interacts with the DNA backbone through charge-charge interactions, and maintains a disordered structure (Coey pg. 10253 left para and fig. 4). The thermophile TDG binds to the DNA target backbone by way of a [4Fe-4S] iron-sulfur cluster (Horst pg. 5460 left col. and Fig. 1 caption), which also interacts with the DNA backbone through charge-charge interactions. This iron-sulfur cluster is on the C-terminus, not the N-terminus, of the thermophile TDG (reference the thermophile TDG structure above). There is no indication in the art that the N-terminal end of the thermophile TDG is associated with DNA binding.
Popov et al. (Reading Targeted DNA Damage in the Active Demethylation Pathway: Role of Accessory Domains of Eukaryotic AP Endonucleases and Thymine-DNA Glycosylases. J Mol Biol. 2020 Mar 13;432(6):1747-1768. Epub 2019 Dec 20) clearly shows that human TDGs have long, disordered, and non-catalytic N- and C-termina often associated with DNA binding affinity (which is supported by Coey), but bacterial TDGs have minimal disordered and non-catalytic N- and C-termina (Popov fig. 1 and pg. 1748 para. 3), and this can be confirmed to be the case with the thermophile TDG based on its protein structure showing only two disordered residues on either terminus (reference structure above).
Coey merely teaches that the sequence termed the “human activator” is essential for the human TDG to function because it is responsible for high affinity, nonspecific DNA binding. This activator sequence is not engineered in any way; it is merely a segment of the human TDG, and Coey characterizes it as such and suggests nothing more. Coey does not teach or suggest that this activator segment of the human TDG can be used for genetic engineering or be "portable", as Applicant termed it, such that it can be fused to a completely different TDG. Coey does not teach or suggest the option of engineering the activator sequence or that it would be able to predictably enhance DNA binding in other proteins other than that human TDG, nor is there any other teaching in the art that would support that concept.
Thus, one of ordinary skill in the art would not conclude that the human activator segment taught by Coey would predictably provide the same advantageous activating effect when bound to the N-terminus of the thermophile TDG taught by Horst, and one of ordinary skill in the art would not have found it obvious to fuse Coey’s human activator segment to the N-terminus of Horst’s thermophile TDG.
Response to Arguments
Applicant’s arguments, see Remarks, filed 24 March 2026, with respect to the 35 USC 103 rejections of claims 1-4, 7, 9, 11, 17, 19-20, and 22-23 have been fully considered and are persuasive. As discussed in the Allowable Subject Matter section above, Examiner agrees that one of ordinary skill in the art would not conclude that the human activator segment taught by Coey would predictably provide the same advantageous activating effect when bound to the N-terminus of the thermophile TDG taught by Horst, and one of ordinary skill in the art would not have found it obvious to fuse Coey’s human activator segment to the N-terminus of Horst’s thermophile TDG.
The rejections under 35 USC 103 of claims 1-3, 7, 9, and 11 over Horst in view of Coey, claim 4 over Horst in view of Coey and Walls, claim 17-19 and 22-23 over Horst in view of Coey and Begley, and claim 20 over Horst in view of Coey, Begley, and Walls have been withdrawn.
Applicant's arguments filed 24 March 2026 with respect to the 35 USC §112(a) written description rejection of claims 2, 17, 19-20, and 22 have been fully considered but they are not persuasive.
Regarding Applicant’s assertion that claims 2 and 17 were amended to recite a “functionally equivalent variant thereof” renders the 112a written description rejection of those claims moot (Remarks pg. 1 sec. II), Applicant’s amendment still does not provide adequate written description for the claimed variants. The claims and the specification paragraphs do not provide sufficient description or indication of what substitutions, insertions, deletions, and/or additions could be tolerated such that the variant polypeptide and/or protein would be considered a functionally equivalent variant. Thus, one of ordinary skill in the art would not be able to recognize if any given amino acid sequence at least 80% identical to SEQ ID NO: 2 would be a functionally equivalent variant or not.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Alexander M Duryee whose telephone number is (571)272-9377. The examiner can normally be reached Monday - Friday 9:00 am - 5:00 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Louise Humphrey can be reached on (571)-272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Alexander M Duryee/Examiner, Art Unit 1657
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
Prosecution Insights