DETAILED ACTION
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 .
Claims 1-8, of record 9/24/2024, are pending and subject to prosecution.
Priority
The instant application is a national stage entry of PCT/JP2023/013138 (filed 3/30/2023). Acknowledgement is made of the applicant’s claim for foreign priority to Japanese application 2022-057755 (filed 3/30/32022).
Specification
The use of the terms jetPEI, Lipofectamine, FuGENE, Attune, NucleoSpin, TruSeq, and iSeq, which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore, the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
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.
Claims 1-8 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.
The term “DNA high-affinity nucleotide analogs” in claims 1-4 is a relative term which renders the claims indefinite. The modifier “high-affinity” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Dependent claims 5-8 are included in the rejection.
Claim Rejections - 35 USC § 103
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.
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.
Claims 1-4 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over Maseda et al. (US 20190284581 A1), of record in IDS dated 9/24/2024, in view of Woolf (US 20190300872 A1).
Regarding claims 1-4 and 8: Maseda et al. teach methods for editing genomic DNA using a single-stranded polynucleotide (See Abstract). The polynucleotide comprises 5’ and 3’ homology arms (which read on “a) a portion capable of hybridizing to the region adjacent to the 3’ terminal side of the primary editing site” and “b) a portion capable of hybridizing to the region adjacent to the 5’ terminal side of the primary editing site”) and can comprise an optional central arbitrary nucleotide sequence to be inserted into the genomic DNA (which reads on “x) an optional portion consisting of a nucleotide sequence that is not identical to the nucleotide sequence of the secondary editing site”) (See fig. 1-2). Somatic cells, which can be human, derived from various tissues (which reads on “ex vivo”) can be editing using the polynucleotide (See ¶0116-0118). The polynucleotide can be provided in a kit (See ¶0051, 0085, and 0158-0160). Maseda et al. teach an embodiment wherein the 5’ and 3’ homology arm lengths range from 43-60 nt and 51-62 nt (which reads on “at least one of portions a) and b) has a length of 32 to 100 nucleotides” and “the other of the portions a) and b) has a length of 10 to 100 nucleotides”) (See table 1). The polynucleotide can comprise LNAs (which read on “DNA high-affinity nucleotide analogs” and “nucleotides in which the oxygen atom at the 2’ position and the carbon atom at the 4’ position of the ribose ring are cross-linked”) (See ¶0141). Maseda et al. do not expressly teach the location of LNAs in the polynucleotide.
Woolf teaches methods for improving genome editing using oligonucleotides with and without programmable nucleases (See Abstract). The editing oligonucleotide can be single-stranded and can comprise modifications that increase stability (See Abstract and ¶0044). The modifications can comprise substitution with LNAs or other modified nucleotides (See ¶0046-0047 and 0068). The oligonucleotide can be modified with LNAs as end-blocking groups for exonuclease resistance (See ¶0232). Modifications can be grouped as about 2-12 successive modifications in the 5’ or 3’ homology arm in order to form a high affinity “seed” region for hybridization, or they can be alternating or occur every third or fourth linkage (which read on “the DNA high-affinity nucleotide analogs are not adjacent to each other”) (See ¶0095).
It would have been obvious to one having ordinary skill in the art prior to the effective filing date of the claimed invention to modify the method of Maseda et al. to comprise LNA modification of the polynucleotide as described by Woolf. One would have been motivated to make this modification in order to promote both hybridization and resistance to exonucleases. Because Maseda et al. teach that the 5’ and/or 3’ homology arm of the polynucleotide can be 10-1000 nt long, preferably 40-70 nt long (See ¶0129-0130), modification of the distal regions of a polynucleotide having ~40 nt arms with LNAs every second, third, or fourth position, as taught by Woolf, could readily encompass the claimed limitation of “at least three DNA high-affinity nucleotide analogs within a range of the 30th to 38th nucleotides, at least one DNA high-affinity nucleotide analogs within a range of the 20th to 29th nucleotides, and no DNA high-affinity nucleotide analog within a ranges of the 1st to 2nd nucleotides or the 7th to 16th nucleotides, in the direction from the terminal adjacent to the other portion of the polynucleotide toward the non-adjacent terminal”.
Allowable Subject Matter
Claims 5-7 would be allowable if rewritten to overcome the rejection under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), 2nd paragraph, set forth in this Office action and to include all of the limitations of the base claim and any intervening claims.
The following is a statement of reasons for the indication of allowable subject matter:
The prior art does not teach or suggest a kit for genome editing comprising two polynucleotides having 5’ or 3’ regions complementary to an overlapping region on opposite genomic DNA strands wherein the overlap length is shorter than the 5’ or ‘3 homology arm of the editing polynucleotide, wherein the editing polynucleotide comprises nucleotide analogs as claimed, and wherein the other polynucleotide is at least 50 nt long.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JENNIFER S SPENCE, whose telephone number is 571-272-8590. The examiner can normally be reached M-F 8:30-5:30.
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/JENNIFER S SPENCE/Examiner, Art Unit 1633
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