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 .
Election/Restrictions
Applicant’s species election of uracil DNA glycosylase in the reply filed on 04/16/2026 is acknowledged.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2 and 9 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 2 depends on claim 1 and adds a limitation describing the abasic site formed as recited in claim 1. Such description simply reiterates what such abasic site formed by action of glycosylase is, without adding any structural differences to such site of claim 1. Therefore, claim 2 does not further limit claim 1.
Claim 9 depends on claim 1 and adds additional steps to step 1 of claim 1, such steps are designing a specific modification site and selecting a non-canonical base, and synthesizing the DNA. Such steps are inherent to step 1 of claim 1, because in order to synthesize a DNA strand carrying a non-canonical base, such base has to be selected and DNA strand has to be synthesized. Therefore, claim 9 does not further limit claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
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.
Claim(s) 1-3, 7-9 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lhomme et al (Biopolymers, 1999, vol.52, pages 65-83).
Concerning claims 1-3, 7-9 Lhomme disclose that DNA glycosylases remove modified or abnormal bases in DNA leading to formation of abasic sites in their place (see page 65, Figures 2 and 7). Lhomme disclose a variety of glycosylases such as uracil DNA glycosylase, which removes uracil residue, wherein such non-canonical base is introduced by solid phase synthesis (see second column on page 66) after designing and selecting the base (see second column on page 66). Further Lhomme disclose that abasic site formed after action of glycosylase is reactive with alkoxyamines (see first column on page 68) such as methoxyamine to form a stable oxime ether (see second column on page 70).
Thus, Lhomme disclose all the steps of instant claim 1, anticipating it. It is noted that preamble of the claim as “method of modifying DNA” is not given patentable weight, therefore it does not need to be taught in prior art.
Claim Rejections - 35 USC § 103
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.
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.
Claim(s) 1-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lhomme et al (Biopolymers, 1999, vol.52, pages 65-83) as applied to claims 1-3, 7-9, and in further view Schaar et al (WO 95/17203, December 1994) and Karp et al (Molecular Tools for Screening Biodiversity, 1998, Chapter 4.2, pages 1-482. Note, because of the size of the document only the copy of first 124 pages is provided).
Lhomme teach that DNA glycosylases remove modified or abnormal bases in DNA leading to formation of abasic sites in their place (see page 65, Figures 2 and 7). Lhomme teach a variety of glycosylases such as uracil DNA glycosylase, which removes uracil residue, wherein such non-canonical base is introduced by solid phase synthesis (see second column on page 66) after designing and selecting the base (see second column on page 66). Other glycosylases are fpg, which removes 8-oxoguanine residue, or alkA, which removes alkylated adenine moieties (see second column on page 71). Further Lhomme teach that abasic site formed after action of glycosylase is reactive with alkoxyamines (see first column on page 68) such as methoxyamine to form a stable oxime ether (see second column on page 70).
Lhomme do not specifically teach using multiple different or same non-canonical bases and different or same glycosylases in the same DNA strand as in instant claims, or separating DNA strand by ethanol precipitation, or desalting DNA strand using desalting column.
Schaar teach separating DNA strand after reaction with glycosylase by ethanol precipitation (see lines 18-26 on page 45).
Karp teach DNA purification using desalting column (see page 59).
It would have been obvious to one of the ordinary skill in the art before the effective filing date of the claimed invention to modify DNA using glycosylases and oxyamine compounds based on teachings of Lhomme, Schaar and Karp, arriving at instant invention. One of the ordinary skill in the art would be motivated to do so because Lhomme teach a variety of glycosylases which are capable of removing specific non-canonical bases in DNA strands, leading to formation of abasic sites, which easily react with oxyamines. One of the art would be motivated to include such same or different non-canonical bases in DNA to be affected by the same or different specific glycosylases to modify DNA based on teachings of Lhomme, because they teach such modifications. Further Schaar and Karp teach specific further steps in DNA purification, which are well known in the art, which can be used in such method of DNA modification.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EKATERINA POLIAKOVA whose telephone number is (571)270-5257. The examiner can normally be reached Mon-Fri 8-5.
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/EKATERINA POLIAKOVA-GEORGANTAS/Primary Examiner, Art Unit 1637
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