DETAILED ACTION
Status of the Claims
Claims 1-7, 9-12, 14-16, 18, 22-23, 25-26, and 28 are currently pending and are the subject of this Office action.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Abstract
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words. It is important that the abstract not exceed 150 words in length since the space provided for the abstract on the computer tape used by the printer is limited. The form and legal phraseology often used in patent claims, such as "means" and "said," should be avoided. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
Currently, the abstract is too short and does not provide enough information to inform of the invention.
Notice of Sequence Noncompliance
Specific deficiency - This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 - 1.825.
The sequence disclosures are located in Fig. 5 and Fig. 9.
Required response – Applicant must provide:
A "Sequence Listing" part of the disclosure, as described above in item 1); as well as
An amendment specifically directing entry of the "Sequence Listing" part of the disclosure into the application in accordance with 1.825(b)(2);
A statement that the "Sequence Listing" includes no new matter in accordance with 1.825(b)(5); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter;
If the "Sequence Listing" part of the disclosure is submitted according to item 1) b), c), or d) above, Applicant must also provide:
A replacement CRF in accordance with 1.825(b)(6); and
Statement according to item 2) a) or b) above.
Drawings (Illegible Text)
The drawings are objected to because the text in Fig. 5 is illegible. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Drawings (Nucleotide Sequences)
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Claim Rejections – 35 U.S.C. 102
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 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Pullmann et al.
Claims 1-3, 5-7, 9, 11-12, 14-16, 18, 22-23, 26, and 28 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pullmann et al. (Scientific Reports, 2019, 9:10932, cited in IDS of 09/27/2022).
Regarding claims 1 and 6-7, Pullmann discloses a method for constructing a large-storage capacity gene mutation library (e.g., Abstract), comprising:
(1) designing and synthesizing two or more oligomer pools having a mutant nucleotide and a restriction site of a restriction endonuclease according to a nucleotide sequence encoding an amino acid sequence which requires library construction (e.g., using BsaI and/or BsbI as per Fig. 1), wherein after digested, two adjacent oligomer pools designed produce same sticky ends (e.g., as per Fig. 1 and in the General concept of Golden Mutagenesis section on pp. 2-3);
(2) amplifying the oligomer pools (e.g., PCR as per Fig. 1 and the General PCR Protocol section on pp. 7-8);
(3) assembling the oligomer pools in a reaction system to obtain an assembled oligomer pool (e.g., as per Fig. 1 and the Case II: Multi-Site-Saturation Mutagenesis. Section on p. 7); and
(4) amplifying the assembled oligomer pool to obtain the large-storage capacity gene mutation library (e.g., via transformation into E. coli and as per Fig. 1).
Regarding claim 2, Pullmann discloses the above method, wherein step (2) comprises: performing PCR amplification on each oligomer pool using a high-fidelity DNA polymerase by taking each oligomer pool as a template and taking the forward primer and reverse primer designed according to the sequence of each oligomer pool as a primer pair, to obtain each amplified oligomer pool (e.g., PCR using Phusion High-Fidelity DNA polymerase as per the General PCR Protocol section on pp. 7-8).
Regarding claim 3, Pullmann discloses the above method, wherein step (3) comprises: adding each amplified oligomer pool, simultaneously adding the restriction endonuclease and a DNA ligase, and assembling each amplified oligomer pool by using a restriction-ligation method to obtain the assembled oligomer pool.
Regarding claim 5, Pullmann discloses the above method, wherein the storage capacity of the gene mutation library is up to 105 (e.g., as per Fig. 4).
Regarding claim 9, Pullmann discloses the above method, wherein step (1) comprises identifying the sticky ends in the coding nucleotide sequence, and dividing the sequence into two or more fragments corresponding to the two or more oligomer pools according to the 3' ends of the sticky ends, then sequentially introducing a reverse complement sequence of a recognition sequence of the restriction endonuclease and a specific sequence 1 at 3' end after a sticky end of a first fragment, to obtain an oligomer pool 1, and sequentially introducing a sticky end, a recognition sequence of the restriction endonuclease and a specific sequence 2 at 5' end of a second fragment, to obtain an oligomer pool 2 (e.g., as per Fig. 1 and in the General concept of Golden Mutagenesis section on pp. 2-3).
Regarding claims 11-12, Pullmann discloses the above method, wherein the sticky end is a single sticky end or a degenerate sticky end, and the number of the oligomer pools is 2-6 (e.g., as per Fig. 1).
Regarding claims 14-15, Pullmann discloses the above method, wherein the GC content of the sticky end is 50%-75% and wherein the sticky end does not contain a palindromic structure (e.g., CTCA as per Fig. 2).
Regarding claim 16, Pullmann discloses the above method, wherein the restriction-ligation method in step (3) is Golden Gate cloning (e.g., as per Fig. 1 and in the General concept of Golden Mutagenesis section on pp. 2-3).
Regarding claims 18 and 26, Pullmann discloses the above method, further comprising (5) recovering and/or purifying the product of the gene mutation library obtained in step (4), to obtain a final library product (e.g., via plasmid preparation prior to sequencing as per the Quick quality control (QQC) of randomization through sequencing section on p. 9).
Regarding claim 22, Pullmann discloses the above method, wherein the number of the mutant nucleotide in each oligomer pool synthesized in step (1) is 1-108 (e.g., as per Fig. 4).
Regarding claim 23, Pullmann discloses the above method, wherein the mutant nucleotide in each oligomer pool synthesized in step (1) encodes a mutation of 1-36 amino acids (e.g., as per Fig. 4).
Regarding claim 28, Pullmann discloses a method for analyzing the relationship between an amino acid mutation in a protein and the property, regulation and/or function of the protein, comprising the following steps:
(1) constructing a gene mutation library by using the method according to claim1;
(2) comparing the property, regulation and/or function of the protein encoded by a mutant gene in the constructed gene mutation library with that of a unmutated protein; and
(3) analyzing the relationship between the amino acid mutation in the protein and the property, regulation and/or function of the protein (e.g., via sequencing to get the encoded protein sequence as per the Quick quality control (QQC) of randomization through sequencing section on p. 9).
Claim Rejections – 35 U.S.C. 103(a)
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 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.
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.
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
Pullmann et al. and Jewett et al.
Claims 1-7, 9-12, 14-16, 18, 22-23, 25-26, and 28 are rejected under 35 U.S.C. 103 as being unpatentable over Pullmann et al. (Scientific Reports, 2019, 9:10932, cited in IDS of 09/27/2022) in view of Jewett et al. (U.S. 9,528,137 B2, issued 12/27/2016).
Pullmann is relied on as above, however, it is noted that the reference is silent to the explicit limitations of wherein step (4) comprises: performing PCR amplification on the assembled oligomer pool using the high-fidelity DNA polymerase by taking the assembled oligomer pool as a template and taking a forward primer of a first oligomer pool and a reverse primer of a last oligomer pool as a primer pair, to obtain the large-storage capacity gene mutation library, wherein the high-fidelity DNA polymerase is Phusion DNA polymerase, as set forth in claims 4 and 25, as well as the specific sequences 1 and 2n-1 being random and not homologous to the original coding nucleotide sequence, as set forth in claim 10.
Jewett discloses methods of cell-free protein expression using PCR products (linear template) and Phusion DNA polymerase (e.g., Abstract and throughout). Use of PCR as final amplification also allows for the use of arbitrary primer binding sequences, since there is no constraint on matching sequencing in cloning sites of an expression vector.
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to amplify the final product using PCR as per Jewett rather than by transformation and plasmid preparation as per Pullmann. One of ordinary skill in the art would have been motivated to do so since, at least in the case of cell-free protein expression platforms, linear DNA template is preferred (e.g., as per col. 17 of Jewett) and Phusion DNA polymerase is known to be a high-fidelity polymerase (e.g., as per col. 25 of Jewett).
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since PCR amplification using Phusion DNA polymerase and subsequent cell-free protein expression was well within reach of the skilled artisan and both could readily be accomplished using well-documented commercially available kits.
Conclusion
No claims are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684