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 11-14 and 16-27 are pending and under examination on their merits. Claim 1-10 and15 are cancelled, rendering moot all rejections of these claims.
The objection to the specification is withdrawn in view of the amendment to the specification filed on 9/19/2025.
The objections to claims 14 and 17-18 are withdrawn in view of the amendment.
Response to Arguments
Applicant's arguments filed 9/19/2025 have been fully considered but they are not persuasive.
Applicant argues that the amendment overcomes the written description rejection of claims under 35 U.S.C. 112(a) because claim 11 does not recite “a derivative or fragment thereof” (Arguments, second to last paragraph on page 7).
In response, the amendment does not overcome the rejection because even though Applicant has removed “a derivative or fragment thereof,” the claims are still directed to a nucleic acid molecule that encodes a thermostable ligase variant (derivative) of SEQ ID NO: 2 (independent claim 11) in terms of amino acid sequence identity or directed to a nucleic acid molecule with at least 60% identity to SEQ ID NO: 1 (independent claim 12), which is also a derivative in terms of sequence identity. The specification and the prior art do not establish a structure-function correlation between the amino acid sequence of the polypeptide and enzymatic activity sufficient for the person of ordinary skill in the art to modify SEQ ID NO: 2 by 58 amino acids (corresponds to 15% of the 387 amino acids in SEQ ID NO: 2). Although the prior art teaches some motifs that are important for function of the Rnl1 family of ligases (see Figure 1 of Blonda cited in the Non-Final Action mailed on mailed on 6/4/2025), the prior art of Omari (cited in the Non-Final Action mailed on mailed on 6/4/2025) teaches that the N- and C-terminal domains are also involved in interactions with ATP (page 1576, left column, paragraph 2), which is required for the activity of a ligase. Therefore, the person of ordinary skill in the art would have been unable to determine which 58 amino acids can be modified without affecting catalytic activity, especially given that N- and C-terminal truncations would have unpredictable effects on enzyme activity. Furthermore, although techniques for codon optimization are well-known in the art (see, for example the Abstract Conclusions of Menzella, Hugo G. "Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli." Microbial cell factories 10.1 (2011): 15.), the person of ordinary skill in the art would have been unable to successfully codon optimize the nucleic acid sequence without knowledge a priori of which amino acid residues are required for catalytic function.
Applicant argues against the rejection of claims under 35 U.S.C. 101 on the grounds that SEQ ID NO: 1 is codon-optimized rather than a naturally-occurring sequence (Arguments, paragraph 3 on page 9).
In response, Applicant has not explained why SEQ ID NO: 1 in Table 2 of the specification is labeled as “DNA sequence of a thermostable ligase enzyme referred to as GBS-3074 ligase. Locus tag Ga0072500_1423074.” A locus tag refers to a specific nucleic acid sequence within the assembled metagenome. As established in the Non-Final Action mailed on 6/4/2025, the sequences within the metagenome are naturally occurring (see paragraph bridging pages 10-11).
Priority
Acknowledgment is made of applicant's claim for foreign priority based on an application filed in the European Patent Office on10/14/2020. It is noted, however, that applicant has not filed a certified copy of the EP 20201876 application as required by 37 CFR 1.55.
Claim Rejections - 35 USC § 112
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.
(New Rejection Necessitated by Amendment) Claims 12, 14, 16, 18, and 27 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 12 recites a codon optimized nucleic acid molecule consisting of the nucleic acid sequence according to SEQ ID NO: 1. However, SEQ ID NO: 1 is a naturally occurring sequence, as evidenced by the instant specification (Table 2 on page 23). Although the specification describes codon-optimizing the sequence for expression in E. coli (see Specification lines 10-13 on page 16), the claimed sequence (SEQ ID NO: 1) is not the codon-optimized sequence because it corresponds directly to the locus tag found in the metagenomic data (see Table 2 on page 23). Therefore, it is unclear how the nucleic acid molecule can be consisting of the nucleic acid sequence according to SEQ ID NO: 1 as well as codon optimized.
Claim 14 does not end in a period, rendering the metes and bounds of the claim indefinite.
Claim 27 recites the method of claim 19, wherein the ligation is performed in” a variety of applications. Claim 27 is indefinite because the list of applications does not contain a conjunction separating “rapid amplification of cDNA ends” and “ligation of single-stranded primer products for PCR,” thus it is unclear whether the list is complete.
Claims 16 and 18 are rejected for depending from a rejected base claim and not rectifying the source of indefiniteness discussed above.
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.
(New Rejection Necessitated by Amendment) Claims 11-14 and 16-27 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 11 recites a codon optimized nucleic acid molecule that encodes a thermostable ligase with at least 85% amino acid sequence identity to SEQ ID NO: 2.
Claim 12 recites a codon optimized nucleic acid molecule consisting of or comprising the nucleic acid sequence according to SEQ ID NO: 1 or a nucleic acid sequence having at least 60% identity thereto.
Claims 11-12 both encompass sequence variants (derivatives) of thermostable ligases.
The specification provides no working examples of a nucleic acid sequence with less than 100% identity to SEQ ID NO: 1 or a nucleic acid sequence encoding a polypeptide with less than 100% identity to SEQ ID NO: 2. Example 1 of the specification discloses that the amino acid sequence of SEQ ID NO: 2 was found by searching previously uncharacterized gene products with protein family homology to T4 Rnl1 in a database (the Joint Genome Institute Integrated Microbial Genomes and Microbiomes) containing sequences from metagenomic sampling studies (Specification, page 16, lines 5-9). The specification discloses that the results were limited to those studies in which sampling was conducted at a geographic location in which thermophilic organisms would be expected to grow (page 16, lines 10-12). The specification discloses that T4 Rnl1 is the founding member of the RNA ligase 1 family of enzymes (Specification, lines 31-32 on page 1).
The crystal structure of a full-length T4 RNl1 has been solved: see Figure 2 (b) (Pascal, Current opinion in structural biology 18.1 (2008): 96-105; cited on the IDS filed on 4/1/2024) and Figure 1 of El Omari et al. (Journal of Biological Chemistry 281.3 (2006): 1573-1579; cited on the IDS filed on 4/1/2024). El Omari teaches that Rnl1 consists of 374 amino acids and is organized into a two-domain structure: the N-terminal region includes an α-helix followed by an antiparallel beta sheet (page 1574, Results and Discussion, right column, bottom paragraph). El Omari teaches that the antiparallel beta sheet may play an important role in the RNl1-catalyzed reaction because two amino acids of this region are involved in hydrogen bonding in the active site (page 1575, left column, bottom paragraph). The remainder of the N-terminal domain consists of twisted antiparallel beta-sheets flanked by alpha-helices (page 1575, right column, bottom paragraph) . El Omari teaches that the C-terminal domain structure is very different among members of the enzyme family (page 1576, left column, top paragraph). The secondary structure of the C-terminal Rnl1 domain consists entirely of α-helices (page 1576, left column, top paragraph). El Omari teaches that the Protein Data Bank contains no structural folds similar to the C-terminal domain of Rnl1 (page 1576, left column, top paragraph).
Blonda teaches the isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 (Blondal et al. Nucleic acids research 33.1 (2005): 135-142.; cited on the IDS filed on 4/1/2024; Abstract). Blonda teaches that the RNA ligase 1 family members include the T4 RNA ligase 1, RM378 bacteriophage, and the RNA ligase part of the pnk/pnl gene (ORF 86) from the baculovirus Autographa californica nucleopolyhedrovirus (ACNV) as well as some other baculoviruses (paragraph bridging pages 135-136). Figure 1 of Blonda illustrates the alignment of four members of the RNA ligase 1 family, highlighting motifs in the protein amino acid sequence. Structural similarity within the family is extremely low, ranging from 9% and 18% overall identity (page 137, right column, top paragraph).
The instant SEQ ID NO: 2 is 31% identical to the ligase from TS2126 (see Table 1 on page 17 of the specification) and 9% identical to the T4 ligase (OA Appendix A of the Non-Final Action mailed on 6/4/2025). SEQ ID NO: 2 of Hjorleifsdottir (US 20050266439 A1) is the thermostable ligase from bacteriophage TS2126 (Abstract) and SEQ ID NO: 3 of Hjorleifsdottir is the Rnl1 ligase from T4. The Clustal omega alignment (a bioinformatic tool for multi-sequence alignment: see Madeira et al. Nucleic Acids Research. 2024 Jul;52(W1):W521-W525; cited in the Non-Final Action mailed on 6/4/2025; page 521, right column, top paragraph) of the ligase from bacteriophage TS2126, the T4 ligase, and the instant SEQ ID NO: 2 demonstrates only 37 identities in the alignment (shown by the asterisks in the alignment, OA Appendix B of the Non-Final Action mailed on 6/4/2025). However, the significance of the remaining 347 amino acids in SEQ ID NO: 2 is unknown in terms of its structure and corresponding activity. In contrast, claim 1 recites “at least 85% amino acid sequence identity,” indicating at as many as 58 amino acids can be substituted.
The prior art does not teach any ligase with at least 85% amino acid sequence identity to SEQ ID NO: 2. Likewise, the prior art does not teach a nucleic acid sequence encoding the ligase with at least 60% amino acid sequence identity to SEQ ID NO: 1.
In summary, although the T4 ligase has been crystallized, other members of the Rnl1 ligase family are highly dissimilar in amino acid sequence. In addition, the presently claimed SEQ ID NO: 2 lacks similarity to both the T4 and TS2126 ligase.
Neither the specification nor the prior art disclose the structure-function relationship between the structure of the claimed thermostable ligase and the function of its ligase activity. In other words, the person of ordinary skill in the art would have been unable to visualize the species of thermostable ligase with at least 85% identity to SEQ ID NO: 2 that retain its ligase activity. The sequence of amino acids of the thermostable ligase that correspond to the catalytic active site of the presently claimed ligase are not disclosed within the specification or taught by the prior art. In addition, the crystal structure of the presently claimed thermostable ligase is not disclosed within the specification or taught by the prior art. Therefore, the person of ordinary skill in the art would not have recognized which variants with at least 85% identity to SEQ ID NO: 2 would have preserved the catalytic activity of the ligase.
Based upon the above analysis, the person of ordinary skill in the art would not have recognized that the inventors were in possession of the claimed genus of nucleic acid molecules encoding a thermostable ligase with at least 85% identity to SEQ ID NO: 2 or the claimed genus of nucleic acid molecules with at least 60% identity to SEQ ID NO: 1 at the time the application was filed.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
(New Rejection Necessitated by Amendment) Claims 12, 16, and 18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to the judicial exception of a product of nature without significantly more. The rationale for this determination is explained below.
A flowchart has been established to determine subject matter eligibility under 35 U.S.C. 101. See MPEP 2106 part (III) and 2106.04 part (II)(A). The flowchart comprises answering: Step 1) Is the claim to a process, machine, manufacture or composition of matter? Step 2A Prong One) Does the claim recite an abstract idea, law of nature or natural phenomenon? Step 2A Prong Two) Does the claim recite additional elements that integrate the judicial exception into a practical application? Step 2B) Does the claim recite additional elements that amount to significantly more than the judicial exception? The claims are analyzed for eligibility in accordance with their broadest reasonable interpretation.
Claim 12 recites a codon optimized nucleic acid molecule consisting of or comprising the nucleic acid sequence according to SEQ ID NO: 1 or a nucleic acid sequence having at least 60% identity thereto.
This rejection applies to the embodiment in which the nucleic acid molecule consists of the nucleic acid sequence according to SEQ ID NO: 1.
SEQ ID NO: 1 is a naturally occurring sequence. Although the specification describes codon-optimizing the sequence for expression in E. coli (see Specification lines 10-13 on page 16), the claimed sequence (SEQ ID NO: 1) is not the codon-optimized sequence because it corresponds directly to the locus tag found in the metagenomic data (see Table 2 on page 23).
The broadest reasonable interpretation of a codon optimized nucleic acid molecule comprising a nucleic acid sequence having at least 60% identity to SEQ ID NO: 1 encompasses nucleic acid sequences with at least 60% identity to SEQ ID NO: 1 but less than 100% identity because SEQ ID NO: 1 is naturally occurring and is thus not codon optimized.
Example 1 of the specification discloses that the amino acid sequence of SEQ ID NO: 2 was found by searching previously uncharacterized gene products with protein family homology to T4 Rnl1 in a database (the Joint Genome Institute Integrated Microbial Genomes and Microbiomes) containing sequences from metagenomic sampling studies (Specification, page 16, lines 5-9). The specification discloses that the results were limited to those studies in which sampling was conducted at a geographic location in which thermophilic organisms would be expected to grow (Specification, page 16, lines 10-12). In other words, the database contains naturally occurring sequences and SEQ ID NO: 2 derives from a sequence identified through sampling a geographic location in which thermophilic organisms would be expected to grow. See also Table 1, which indicates that the locus tag corresponding to SEQ ID NO: 1 originates from Great Boiling Spring, Nevada, which is a natural source (page 17, line 5; the nucleic acid SEQ ID NO: 1 encodes the amino acid SEQ ID NO: 2).
Claim 12 is drawn to a composition of matter, which is one of the four statutory categories of invention (Step 1: Yes). Claim 12 recites the judicial exception of a product of nature, which is the naturally occurring nucleic acid found in the metagenome: see Table 2, SEQ ID NO: 1 (Step 2A, Prong One: Yes). Although the specification describes codon-optimizing the sequence for expression in E. coli (see Specification lines 10-13 on page 16), the claimed sequence (SEQ ID NO: 1) is not the codon-optimized sequence because it corresponds directly to the locus tag found in the metagenomic data (see Table 2 on page 23). The judicial exception is not integrated into a practical application (Step 2A, Prong Two: No). Claim 16 is drawn to an expression vector comprising the nucleic acid sequence and claim 18 is drawn to a kit comprising the nucleic acid sequence. However, there are no additional elements recited in the kit besides the nucleic acid sequence (Step 2B: No) and expression of a gene within a vector is well-understood, routine, and conventional (Step 2B: No): see IDT (website, 2025; “What is an expression vector”; cited in the Non-Final Action mailed on 6/4/2025).
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 CANDICE LEE SWIFT whose telephone number is (571)272-0177. The examiner can normally be reached M-F 8:00 AM-4:30 PM (Eastern).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Louise Humphrey can be reached at (571)272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657