DETAILED ACTION
Response to Amendment
Applicant’s response to the office action filed on August 21, 2025 has been entered. The claims pending in this application are claims 53-72, 74, 76-84, and 86-90 wherein claims 53-70 and 78 have been withdrawn due to the restriction requirement mailed on May 27, 2022. The objection not reiterated from the previous office action is hereby withdrawn in view of applicant’s amendment filed on August 21, 2025. Claims 71, 72, 74, 76, 77, 79-84, and 86-90 will be examined.
Claim Objections
Claim 89 is objected to because of the following informalities: (1) “the variant nucleic acid library” should be “the nucleic acid library” in view of claim 82; and (2) the word “respective” in last line should be deleted.
Appropriate correction is required.
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.
Claims 71, 72, 74, 76, 77, 79-84, and 86-90 are rejected under 35 U.S.C. 103 as being unpatentable over Duchateau et al., (US 2010/0021448 A1, published on January 28, 2010) in view of Skulachev et al., (US 2012/0259110 A1, published on October 11, 2012).
Regarding claims 71, 72, 76, 77, and 79-81, since claim 71 does not indicate the sizes of a nucleic acid library of a nucleic acid molecule of interest, the first target region and the second target region, claim 72 does not indicate the size of a third or further target region, claim 80 does not indicate the size of a third, fourth, fifth or sixth or further target region, and the nucleic acid mutant library taught by Duchateau et al., encodes more than 100 different I-Cre I meganuclease variants with amino acid mutations are located on their positions 44, 68, and 70 (see paragraphs [0066], [0069], and [0088]), it is reasonable to consider that a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 40 to 46 of I-Cre I meganuclease is a first target region, a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 62 to 68 of I-Cre I meganuclease is a second target region, and a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease is a third target region. Thus, Duchateau et al., teach a variant nucleic acid library of a nucleic acid molecule of interest (eg., a variant nucleic acid library encoding 3 different I-Cre I meganuclease variants or more than 100 different I-Cre I meganuclease variants), wherein the nucleic acid molecule comprises a first target region (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 40 to 46 of I-Cre I meganuclease) and a second target region (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 62 to 68 of I-Cre I meganuclease), wherein each of the first target region and the second target region is a pre-defined region of the nucleic acid molecule that can be hybridised using an oligonucleotide primer (ie., the pre-defined region of the nucleic acid molecule has an ability to hybridize to an oligonucleotide primer); wherein the library comprises nucleic acid variants of the nucleic acid molecule of interest (ie., different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70), wherein each of the nucleic acid variants of the nucleic acid molecule of interest is a variant comprising the first target region and of the second target region of the nucleic acid molecule of interest, wherein each of the nucleic acid variants of the nucleic acid molecule of interest encodes a protein variant (ie., one of I-Cre I meganuclease variants), and wherein each of
the nucleic acid variants of the nucleic acid molecule of interest comprises i) an OR-type mutation in each of the first target region wherein said OR type mutation is a mutation which is not shared by the other nucleic acid variants of the first target region of the nucleic acid molecule of interest; and ii) an OR type mutation in the second target region, wherein said OR type mutation is a mutation which is not shared by the other nucleic acid variants of the second target region of the nucleic acid molecule of interest; such that each nucleic acid variant of the nucleic acid library comprises a combination of mutations which is not shared by the other variants of the nucleic acid library as recited in claim 71 wherein each variant of the variant nucleic acid library comprises an OR-type mutation in a third (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease) or further target region as recited in claim 72, each variant of the variant nucleic acid library comprises an OR-type mutation in two or more target regions and a mutation in one or more other target regions as recited in claim 76, the variant nucleic acid library comprises a physical library that is smaller than a theoretical library (ie., any kind of nucleic acid library made by a human brain or a computer) as recited in claim 77, an amplification product of a target region can serve as a primer in an amplification reaction (ie., an amplification product of a target region has an ability to serve as a primer in an amplification reaction) as recited in claim 79, a variant of the nucleic acid library comprises a third (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease), fourth, fifth or sixth or further target region, and the variant comprises an OR-type mutation of the third, fourth, fifth or sixth or further target region as recited in claim 80, and the nucleic acid library has a physical size of about 100 variants (ie., 100 different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70) or more as recited in claim 81 (see paragraphs [0007], [0066], [0069], [0088]), and [0141] to [0151], and claim 1-22, 39, and 40).
Regarding claims 82, 83, and 86-90, since claim 82 does not indicate the sizes of a nucleic acid library of a nucleic acid molecule of interest, the first target region and the second target region, claim 83 does not indicate the size of a third or further target region, claim 89 does not indicate the size of a third, fourth, fifth or sixth or further target region, and the nucleic acid mutant library taught by Duchateau et al., encodes more than 100 different I-Cre I meganuclease variants with amino acid mutations are located on their positions 44, 68, and 70 (see paragraphs [0066], [0069], and [0088]), it is reasonable to consider that a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 40 to 46 of I-Cre I meganuclease is a first target region, a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 62 to 68 of I-Cre I meganuclease is a second target region, and a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease is a third target region. Thus, Duchateau et al., teach a nucleic acid library of a nucleic acid molecule of interest (eg., a variant nucleic acid library encoding 3 different I-Cre I meganuclease variants or more than 100 different I-Cre I meganuclease variants), wherein the nucleic acid molecule comprises a first target region and a second target region, wherein each of the first target region (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 40 to 46 of I-Cre I meganuclease) and the second target region (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 62 to 68 of I-Cre I meganuclease) is a pre-defined region of the nucleic acid molecule that can be hybridised using an oligonucleotide primer (ie., the pre-defined region of the nucleic acid molecule has an ability to hybridize to an oligonucleotide primer); wherein the library comprises nucleic acid variants of the nucleic acid molecule of interest (ie., different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70),wherein each of the nucleic acid variants of the nucleic acid molecule of interest is a variant comprising the first target region and of the second target region, wherein each of the nucleic acid variants of the nucleic acid molecule of interest encodes a protein variant (ie., one of I-Cre I meganuclease variants), wherein each of the nucleic acid variants of the nucleic acid molecule of interest comprises 1) an alternate mutation in the first target region wherein said alternate mutation is a mutation which is not shared by the other nucleic acid variants of the first target region of the nucleic acid molecule of interest; and ii) an alternate mutation in the second target region, wherein said an-alternate mutation is a mutation that is not shared by the other nucleic acid variants of the nucleic acid molecule of interest of the nucleic acid molecule of interest, such that each nucleic acid variant of the nucleic acid library comprises a combination of mutations which is not shared by the other variants of the nucleic acid library as recited in claim 82 wherein each variant of the variant nucleic acid library comprises an alternate mutation in a third (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease) or further target region as recited in claim 83, each variant of the variant nucleic acid library comprises an alternate mutation in two or more target regions and a mutation in one or more other target regions as recited in claim 86, the variant nucleic acid library comprises a physical library that is smaller than a theoretical library (ie., any kind of nucleic acid library made by a human brain or a computer) as recited in claim 87, an amplification product of a target region can serve as a primer in an amplification reaction (ie., an amplification product of a target region has an ability to serve as a primer in an amplification reaction) as recited in claim 88, each variant of the nucleic acid library comprises a third (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease), fourth, fifth or sixth or further target region, and the each variant of the nucleic acid library comprises an alternate mutation of the third, fourth, fifth or sixth or further target region as recited in claim 89, and the nucleic acid library has a physical size of about 100 variants (ie., different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70) or more as recited in claim 90 (see paragraphs [0007], [0066], [0069], [0088]), and [0141] to [0151], and claim 1-22, 39, and 40).
Regarding claims 74 and 84, since the amino acid in position of 70 of I-Cre I meganuclease is Asp with a genetic code GAT (see paragraph [0141] and SEQ ID No. 69), amino acid in position of 70 of variant A44/A68/A70 is Ala with a genetic code GCT, the amino acid in position of 70 of variant D44/R68/G70 is Gly with a genetic code GGC, and the amino acid in position of 70 of variant K44/ N68/S70 is Ser with a genetic code TCC, changing Asp in position of 70 of I-Cre I meganuclease to Ala, Gly, and Ser requires to change one nucleotide, two nucleotides, and three nucleotides in its genetic code respectively. Thus, Duchateau et al., teach that each nucleic acid variant of the variant nucleic acid library (ie., a variant nucleic acid library encoding 3 different I-Cre I meganuclease variants such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70) comprises a different number (eg., 1 to 3) of OR-type mutations in any one target region (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease) as recited in claim 74 and each nucleic acid variant of the variant nucleic acid library (ie., a variant nucleic acid library encoding 3 different I-Cre I meganuclease variants such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70) comprises a different number (eg., 1 to 3) of alternate mutations in any one target region (ie., a nucleotide sequence of I-Cre I meganuclease cDNA encoding an amino acid sequence from position 69 to 75 of I-Cre I meganuclease) as recited in claim 84.
Duchateau et al., do not disclose a single sample comprising a nucleic acid library of a nucleic acid molecule of interest as recited in claims 71 and 82.
Skulachev et al., teach to construct a sublibrary by selecting substances with the desired biological activity from a library (see paragraph [0124]).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have made the single sample comprising a nucleic acid library of a nucleic acid molecule of interest recited in claim 71 or 82 by selecting different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70 from more than 100 different I-Cre I meganuclease variants taught by Duchateau et al., and forming a single sample by putting the selected different I-Cre I meganuclease variants together in view of the prior arts of Duchateau et al., and Skulachev et al.. One having ordinary skill in the art would have been motivated to do so because Skulachev et al., teach to construct a sublibrary by selecting substances with the desired biological activity from a library (see paragraph [0124]). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to make the single sample comprising a nucleic acid library of a nucleic acid molecule of interest recited in claim 71 or 82 by selecting different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70 from more than 100 different I-Cre I meganuclease variants taught by Duchateau et al., and forming a single sample by putting the selected different I-Cre I meganuclease variants together in view of the prior arts of Duchateau et al., and Skulachev et al., in order to construct a sublibrary comprising different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70.
Response to Arguments
In page 10, third paragraph bridging to page 14, second paragraph of applicant’s remarks, applicant argues that “[F]irst, neither Duchateau nor Skulachev teach, suggest, or disclose a single sample comprising a nucleic acid library comprising inter alia Boolean OR-type or alternate mutations as presently claimed. As explained in the previous response, in Duchateau, both the original nucleic acid library (which is the result of the methodology of paragraphs [0141]-[0151]) and the selection of 292 amino acid variants listed in paragraph [0066] comprise mutations which are also present in the other nucleic acid variants. For example, paragraph [0066] indicates that the variants include multiple nucleic acid molecules comprising the A44 mutation, the A68 mutation, the D68 mutation, etc. Thus, this selection of nucleic acid molecules in paragraph [0066] does not satisfy the limitations recited in claims 71 and 82 that require an OR mutation, which is a mutation which is not shared by the other members of the nucleic acid library. Skulachev fails to remedy this deficiency of Duchateau, and fails to teach, suggest, or disclose a single sample comprising a nucleic acid library comprising inter alia Boolean OR- type or alternate mutations as presently claimed. Skulachev 1s limited to chemical compounds of Formula (1), wherein the substituents Y, R1 and R2 are defined. Skulachev does not describe how the library is constituted, for example in terms of the number of compounds, the diversity of compounds made, or the combination of compounds. There is certainly no disclosure that any ‘variant’ substituent (Y, R1 or R2) is not shared by the other variants of the library. Indeed, as is apparent from the structures shown at paragraph [0112], this is clearly not the case. Importantly, Skulachev does not specify that the ‘variant’ substituents (Y, R1, or R2) are not shared by the other variants of the library. To the contrary, the disclosure of Skulachev provides evidence that substituents (e.g., the decyl triphenylphosphonium moiety) are indeed shared (see paragraph [0112] of Skulachev). Thus, Skulachev fails to teach, suggest, or disclose a single sample comprising a nucleic acid library comprising inter alia Boolean OR-type or alternate mutations as presently claimed. Second, Skulachev fails to teach or suggest the provision of a Boolean OR-type library in a single sample. At p. 8, the Office Action points to paragraph [0124] of Skulachev as teaching construction of a sub-library by selecting substances with the desired biological activity from a library, wherein the Office Action appears to interpret the sub-library as being selected compounds from the full library of Skulachev, in a single sample. However, Applicant respectfully disagrees and submits that Skulachev does not teach that the compounds of either the full library or the sub-library are provided in a single sample as required by present claims 71 and 82. Instead, paragraph [0124] describes a method of testing for the biological activity of compounds of the library in order to select compounds with the desired activity to create the sub- library. The method comprises the steps of: (1) screening the whole library individually; (2) taking positive compounds from this first screen to create a combinatorial sub-library; (3) testing the compounds of the sub-library for the desired activity; and 4) repeating steps 1-3. There is no disclosure in paragraph [0124], or elsewhere in Skulachev, that the full library or the sub-library are provided in a single sample. Instead, the final sentence of paragraph [0125] specifically states that the compounds are tested in ‘individual test tubes’ (i.e., multiple), and references the Test methods, which are described in Section 4 (paragraphs [0126]-[0135]) and in the Examples. These methods include testing the redox properties and stability (see Example 1), the penetrating ability on artificial black membranes (see Example 2), the protecting or damaging effect (see Example 3), and the antioxidant effect (see Example 4). Whilst paragraph [0125] states that the methods can be adapted for combinatorial libraries, there is no disclosure or suggestion that this may be achieved by providing the library of compounds in a single sample. Rather, the disclosure suggests ‘highly productive methods’ for testing a combinatorial library, which would be interpreted by one of ordinary skill in the art as high throughput testing i.e., performing a single sample test repeatedly in order to individually test the full combinatorial library. If testing were performed using a pooled sample of multiple compounds, the activity of an individual compound could not be discerned, which renders Skulachev inoperative for its intended purpose, i.e., identifying/selecting individual compounds based on their antioxidant activities. An interpretation of Skulachev whereby all of the compounds to be tested are provided in a single sample would not technically align with the testing methods suggested” and “in view of Examples 1-4 described above and paragraph [0125] of Skulachev, it is apparent that the compounds of the library in Skulachev are not provided in a single sample. Rather, Skulachev teaches the synthesis of a panel of compounds which are tested separately and are not provided together in a single sample. It is important to note that the methodology described in testing mixtures described in paragraphs [0126]-[0135] and certain Examples of Skulachev for the desired activity would not provide data for individual compounds, because there is no teaching as to how to distinguish the compounds from each other in the testing methods used. It would therefore not be obvious from the teaching of Skulachev to provide a single sample comprising a nucleic acid library of a nucleic acid molecule of interest.
Third, one of ordinary skill in the art would not be motivated to combine the teachings of Duchateau and Skulachev to arrive at the present claims. Skulachev relates to organic compounds that function as mitochondria-addressed antioxidants, which are a different type of molecular compound from nucleic acids. One of ordinary skill in the art would understand that preparation and screening of a nucleic acid library requires a different technical approach than screening a library of chemical entities. As such, one of ordinary skill in the art would not look to Skulachev to remedy any perceived deficiency of Duchateau. Finally, evidence of unobvious or unexpected properties can rebut prima facie obviousness. The provision of the variant nucleic acid library of the present invention in a single sample has the technical advantages of reducing the library size, such that the physical size of the library is smaller than the theoretical size (see present claim 77). Given that this result is not disclosed, taught, or suggested by Duchateau or Skulachev, the result is unexpected. The provision of the members of the library in a single sample has advantages in terms of screening efficiency, as well as improved efficiencies in storage, handling and supply”.
These arguments have been fully considered but they are not persuasive toward the
withdrawal of the rejection.
First, the rejection is not dependent either a prior art from Duchateau et al., or a prior art from Skulachev et al., alone but is based on a combination of the prior art from Duchateau et al., and the prior art from Skulachev et al..
Second, although applicant argues that “in Duchateau, both the original nucleic acid library (which is the result of the methodology of paragraphs [0141]-[0151]) and the selection of 292 amino acid variants listed in paragraph [0066] comprise mutations which are also present in the other nucleic acid variants. For example, paragraph [0066] indicates that the variants include multiple nucleic acid molecules comprising the A44 mutation, the A68 mutation, the D68 mutation, etc. Thus, this selection of nucleic acid molecules in paragraph [0066] does not satisfy the limitations recited in claims 71 and 82 that require an OR mutation, which is a mutation which is not shared by the other members of the nucleic acid library” and “[S]kulachev fails to teach or suggest the provision of a Boolean OR-type library in a single sample”, since Duchateau et al., teach different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70 (see paragraph [0066]) and Skulachev et al., teach to construct a sublibrary by selecting substances with the desired biological activity from a library (see paragraph [0124]), one having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to make the single sample comprising a nucleic acid library of a nucleic acid molecule of interest recited in claim 71 or 82 by selecting different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70 from more than 100 different I-Cre I meganuclease variants taught by Duchateau et al., and forming a single sample by putting the selected different I-Cre I meganuclease variants together in view of the prior arts of Duchateau et al., and Skulachev et al., in order to construct a sublibrary comprising different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70.
Third, although applicant argues that “Skulachev relates to organic compounds that function as mitochondria-addressed antioxidants, which are a different type of molecular compound from nucleic acids. One of ordinary skill in the art would understand that preparation and screening of a nucleic acid library requires a different technical approach than screening a library of chemical entities”, since Skulachev et al., teach to construct a sublibrary by selecting substances with the desired biological activity from a library (see paragraph [0124]), the same concept for constructing a sublibrary from a library taught by Skulachev et al., will be used for constructing a sublibrary comprising different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 by selecting different I-Cre I meganuclease variants with different amino acids in each of their positions 44, 68, and 70 such as A44/A68/A70, D44/R68/G70, and K44/ N68/S70 from more than 100 different I-Cre I meganuclease variants taught by Duchateau et al..
Fourth, although applicant argues that “[T]he provision of the variant nucleic acid library of the present invention in a single sample has the technical advantages of reducing the library size, such that the physical size of the library is smaller than the theoretical size (see present claim 77). Given that this result is not disclosed, taught, or suggested by Duchateau or Skulachev, the result is unexpected. The provision of the members of the library in a single sample has advantages in terms of screening efficiency, as well as improved efficiencies in storage, handling and supply”, since a collection of genetic material fragments can be considered as a library and constructing a nucleic acid sublibrary from a nucleic acid library is well known in the art (see pages 850-852 and Figure 1 from Ellington et al., Nature, 355, 850-852, 1992 wherein single stranded DNA molecules that fold into specific ligand-binding structures are selected from 157-base oligomer containing 120 bases of random sequence flanked by defined primer-binding sites), based on reducing the library size, a nucleic acid sublibrary made from a nucleic acid library is expected to have “advantages in terms of screening efficiency, as well as improved efficiencies in storage, handling and supply” as stated by applicant.
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.
No claim is allowed.
Papers related to this application may be submitted to Group 1600 by facsimile transmission. Papers should be faxed to Group 1600 via the PTO Fax Center. The faxing of such papers must conform with the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993)(See 37 CAR § 1.6(d)). The CM Fax Center number is (571)273-8300.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph.D., whose telephone number is (571)272-0746. The examiner can normally be reached on Monday-Friday from 9 A.M. to 5 P.M.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Dr. Anne Gussow, Ph.D., can be reached on (571)272-6047.
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/FRANK W LU/Primary Examiner, Art Unit 1683 October 24, 2025