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 .
Status of Claims
Receipt of Arguments/Remarks filed on 8/6/2025 is acknowledged. No claims were amended. Claims 1-5 are pending.
Information Disclosure Statement
The information disclosure statement (IDS) filed on 6/30/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Withdrawn Objections
The amendment filed 8/6/2025 is sufficient to overcome the objection to the specification.
Maintained Rejections
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-5 are rejected under 35 U.S.C. 103 as being unpatentable over Miller et al.,
Nature biotechnology; 29(2):143-8 in view of Koussevitzky et al., Science; 316(5825):715-9 and
Small et al., Trends in biochemical sciences; 25(2):45-7.
Regarding claim 1, Miller teaches a method of targeted gene editing of a cell using
DNA binding TALE proteins (Miller pg. 143 Abstract and para. 1-4). Miller teaches designing
TALE proteins that selectively bind to target DNA (Miller pg. 144 Figs. 1 and 2). Miller further
teaches designing a TALE-nuclease chimera (TALEN) with a DNA binding region, TALE, and a
functional region, the catalytic domain of DNA-cleaving Fokl enzyme (Miller pg. 145 "Development of a TALE-nuclease architecture" and pg. 147 "Discussion"). Miller teaches
cloning this DNA sequence and preparing a vector with the DNA sequence (Miller pg. 149 "TALE constructs"). Miller also teaches a cell with a target DNA base sequence of at least 9 bp,
HEK293 cells, and introducing the vector into the cells for targeted gene editing (Miller pg. 143
para. 4; pg. 146 Fig. 4; and pg. 149 "Endogenous gene activation assay for NTF3").
Miller does not teach that the DNA-binding protein has at least 9 PPR motifs with a
structure of (Helix A)-X-(Helix B)-L or with position numbers according to the definitions set forth
in claim 1.
However, Koussevitzky teaches a protein from Arabidopsis thaliana with PPR repeats,
GUN1, encoding a 918-amino acid polypeptide (Koussevitzky pg. 715 "GUN1 encodes a
chloroplast-localized pentatricopeptide-repeat protein"). Koussevitzky teaches that GUN1
containing PPR motifs binds DNA, and the sequence of GUN1 is 100% identical to the GUN1
amino acid sequence of instant SEQ ID NO: 2 (Koussevitzky Figs. S1 and S2A, see GUN1
sequence, accession NP_ 180698.1, appended to Koussevitzky ref). Koussevitsky does not
teach that the DNA-binding protein has a structure of (Helix A)-X-(Helix B)-L.
However, Small teaches that PPR motifs from Arabidopsis thaliana form a structure with
two α-helices, corresponding with (Helix A)-X-(Helix B)-L wherein Helix A forms an α-helix, X
does not exist or is 1-9 amino acids, Helix B forms an α-helix, and L is 2-7 amino acids (Small
Fig. 1). Therefore, the PPR motifs of GUN1 as taught by Koussevitzky would be expected to
have this structure.
The limitation "wherein position numbers of amino acids in the PPR motifs are the same
as PF01535 in Pfam under the following definitions" states rules for defining the position number of amino acids in a PPR motif, which are known in the art according to PF01535. These position numbers can be applied to any PPR motif having the structure as claimed, and therefore the PPR motifs taught by Koussevitzky and Small meet this limitation. Koussevitzky additionally teaches the elected species, option (2-22), wherein the combination of amino acids in the PPR motif is an arbitrary amino acid at Number 1 AA, and asparagine at Number 4 AA and Number ii AA. According to Table 2 in the instant specification, the PPR motif of GUN1 having this combination is PPR motif 5, with F at position 375, N at position 378, and N at position 408. Koussevitsky teaches a sequence that is 100% identical to SEQ ID NO: 2, GUN1, and therefore Koussevitsky also teaches this combination of amino acids at these positions (Koussevitzky Fig. S1).
It would have been obvious to a skilled artisan, before the effective filing date, to
combine the teachings of Miller, Koussevitzky, and Small, arriving at a method for modifying the
genetic substance of a cell as instantly claimed. Genetic modification using DNA-binding
proteins is known in the art as taught by Miller. Given the teachings of Koussevitzky that GUN1
is known to be a DNA-binding protein comprising PPR motifs, it would have been obvious to a
skilled artisan to substitute the DNA-binding region taught by Miller for the DNA-binding PPR
motifs taught by Koussevitzky and Small.
A person of ordinary skill in the art would have been motivated to combine the teachings
of these references and incorporate a PPR motif in the method of gene editing taught by Miller
because PPR proteins are known to function in editing of nucleic acid sequences, including
DNA, and GUN1 has an SMR domain which is found in proteins associated with DNA repair and
recombination (Koussevitzky pg. 715 col. 3).
A skilled artisan would have a reasonable expectation of success in making this
substitution to achieve the predictable outcome of targeted gene editing using a DNA-binding
PPR motif from GUN1, given the successful use of a DNA-binding protein for gene editing as
taught by Miller, and the known DNA-binding activity of PPR protein GUN1 taught by
Koussevitzky.
Regarding claim 2, Miller teaches a TALEN with TALE repeats and a C-terminal
functional region, Fokl cleavage domain (Miller pg. 149 "TALE constructs").
Regarding claims 3 and 4, Miller teaches that the functional region is a DNA-cleaving
enzyme cleavage domain, Fokl (Miller pg. 149 "TALE constructs").
Regarding claim 5, Koussevitzky teaches GUN1, which is identical to instant SEQ ID
NO: 2 (Koussevitzky Figs. S1 and S2A, see GUN1 sequence appended to Koussevitzky ref).
Double Patenting
The non statutory double patenting rejection is based on a judicially created doctrine
grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or
improper timewise extension of the "right to exclude" granted by a patent and to prevent
possible harassment by multiple assignees. A nonstatutory double patenting rejection is
appropriate where the conflicting claims are not identical, but at least one examined application
claim is not patentably distinct from the reference claim(s) because the examined application
claim is either anticipated by, or would have been obvious over, the reference claim(s). See,
e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d
1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Langi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir.
1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d
438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA
1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321 (c) or 1.321 (d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting
provided the reference application or patent either is shown to be commonly owned with the
examined application, or claims an invention made as a result of activities undertaken within the
scope of a joint research agreement. See MPEP § 717.02 for applications subject to
examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159.
See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to
file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR
1.321 (b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory
double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be
accompanied by a reply requesting reconsideration of the prior Office action. Even where the
NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1.
For a reply to a non-final Office action, see 37 CFR 1.111 (a). For a reply to final Office action,
see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c)
may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used.
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Claims 1-5 are provisionally rejected on the ground of nonstatutory double patenting
as being unpatentable over claims 1, 3, and 4 of copending Application No. 17/365,292
(reference application) in view of Miller et al., Nature biotechnology; 29(2):143-8.
Regarding instant claim 1, claim 1 of copending '292 discloses a method for designing
a DNA binding protein by determining the sequence of a DNA binding protein, wherein the
protein has the structure of formula 1 as instantly claimed and the amino acid positions are
defined as set forth in instant claim 1. Claim 3 of copending '292 discloses a method for
preparing a DNA binding protein of claim 1 by determining a nucleic acid sequence, cloning the
nucleic acid sequence, and preparing a transformant producing the DNA binding protein. Claims
1 and 4 of copending '292 disclose at least 9 PPR motifs. The claims of copending '292 do not disclose a method for modifying the genetic substance of a cell using the DNA binding protein,
or a functional region in addition to a DNA binding region.
Miller teaches a method of targeted gene editing of a cell using DNA binding TALE proteins (Miller pg. 143 Abstract and para. 1-4). Miller teaches designing TALE proteins that selectively bind to target DNA (Miller pg. 144 Figs. 1 and 2). Miller further teaches designing a TALE-nuclease chimera (TALEN) with a DNA binding region, TALE, and a functional region, the catalytic domain of DNA-cleaving Fokl enzyme (Miller pg. 145 "Development of a TALE nuclease architecture" and pg. 147 "Discussion"). Miller teaches cloning this DNA sequence and preparing a vector with the DNA sequence (Miller pg. 149 "TALE constructs"). Miller also teaches a cell with a target DNA base sequence of at least 9 bp, HEK293 cells, and introducing the vector into the cells for targeted gene editing (Miller pg. 143 para. 4; pg. 146 Fig. 4; and pg. 149 "Endogenous gene activation assay for NTF3").
It would have been obvious to a person having ordinary skill in the art to combine the
teachings of Miller with copending '292. Both teach DNA binding proteins that bind DNA in a
sequence specific manner. A skilled artisan would recognize that the DNA binding protein
taught by copending '292 could be used in combination with a functional domain as taught by
Miller for targeted gene editing, as this would require only a substitution of one known DNA
binding protein for another.
Regarding instant claims 2-4, copending '292 does not teach a functional region fused
to the C-terminus side of the protein, that the functional region is any of those recited in instant
claim 3, or that the DNA cleaving enzyme is Fok1.
However, Miller teaches a TALEN with TALE repeats and a C-terminal functional region,
Fokl cleavage domain (Miller pg. 149 "TALE constructs"). Miller additionally teaches that the
functional region is a DNA-cleaving enzyme cleavage domain, Fokl (Miller pg. 149 "TALE
constructs"). It would have been obvious to a person having ordinary skill in the art to combine the teachings of Miller with copending '292 as set forth above, further incorporating the specific
DNA cleaving enzyme for DNA modification as taught by Miller.
Regarding instant claim 5, claim 4 of copending '292 discloses that the PPR motifs are
chosen from among the same PPR motifs recited in instant claim 5.
For these reasons, instant claims 1-5 are an obvious variation of claims 1, 3, and 4 of
copending Application No. 17/365,292 in view of Miller.
This is a provisional nonstatutory double patenting rejection.
Claims 1-5 are provisionally rejected on the ground of nonstatutory double patenting
as being unpatentable over claim 1, 3, 4, and 7-8 of copending Application No. 18/035,430 in
view of Koussevitzky et al., Science; 316(5825):715-9 and Small et al., Trends in biochemical
sciences; 25(2):45-7.
Regarding instant claims 1-5, claim 1 of copending '430 discloses a Fok1 protein
nuclease domain mutant. Claim 3 discloses an artificial nucleic acid cleaving enzyme
comprising a nucleic acid binding domain and the nuclease domain mutant according to claim 1.
Claim 4 discloses that the nucleic acid binding domain is PPR (pentatricopeptide repeat).
Claims 7 and 8 disclose a method for gene editing using a cell with the nucleic acid cleaving
enzyme introduced. Copending '430 does not teach the PPR motif according to the definitions
of instant claim 1 or that the PPR motif is selected from among those in instant claim 5.
However, Koussevitzky teaches a protein from Arabidopsis thaliana with a PPR repeat
domain, GUN1, encoding a 918-amino acid polypeptide (Koussevitzky pg. 715 "GUN1 encodes
a chloroplast-localized pentatricopeptide-repeat protein"). Koussevitzky teaches that GUN1
containing PPR domains binds DNA, and the sequence of GUN1 is 100% identical to instant
SEQ ID NO: 2 (Koussevitzky Figs. S1 and S2A, see GUN1 sequence appended to
Koussevitzky ref). Koussevitsky does not teach that the DNA-binding protein has a structure of
(Helix A)-X-(Helix B)-L.
However, Small teaches that PPR motifs from Arabidopsis thaliana form a structure with
two α-helices, corresponding with (Helix A)-X-(Helix B)-L wherein Helix A forms an α-helix, X
does not exist or is 1-9 amino acids, Helix B forms an α-helix, and L is 2-7 amino acids (Small
Fig. 1). Therefore, the PPR motifs of GUN1 as taught by Koussevitzky would be expected to
have this structure.
The limitation "wherein position numbers of amino acids in the PPR motifs are the same
as PF01535 in Pfam under the following definitions" states rules for defining position number of
amino acids in a PPR motif, which are known in the art according to PF01535. These position
numbers can be applied to any PPR motif having the structure as claimed, and therefore the
PPR motifs taught by Koussevitzky and Small meet this limitation.
Koussevitzky additionally teaches the elected species, option (2-22), wherein the
combination of amino acids in the PPR motif is an arbitrary amino acid at Number 1 AA, and
asparagine at Number 4 AA and Number ii AA. According to Table 2 in the instant specification,
the PPR motif of GUN1 having this combination is PPR motif 5, with F at position 375, N at
position 378, and N at position 408. Koussevitsky teaches a sequence that is 100% identical to
SEQ ID NO: 2, GUN1, and therefore Koussevitsky also teaches this combination of amino acids
at these positions (Koussevitzky Fig. S1).
It would have been obvious to a skilled artisan to combine the teachings of copending
'430, Koussevitzky, and Small, arriving at a method for modifying the genetic substance of a cell
as instantly claimed. All of these references are directed to PPR motifs with nucleic acid binding
ability. It would have been obvious to use the DNA binding PPR motif GUN1 as taught by
Koussevitzky and Small in the gene editing method of copending '430, which recites the use of
PPR nucleic acid binding domains.
For these reasons, instant claims 1-5 are an obvious variation of claims 1, 3, 4, and 7-8
of copending Application No. 18/035,430 in view of Koussevitzky and Small.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
Applicant's arguments filed 8/6/2025 have been fully considered but they are not persuasive.
Rejections Under 35 U.S.C. § 103
Applicant argues that Small fails to teach that PPR motifs bind to DNA, and while Koussevitzky suggests a fragment of GUN1 containing the PPR can bind to DNA, there is no analysis of which PPR motifs bind to a specific target DNA base.
In response to this argument, it is noted that the instant invention is directed to a method of modifying a genetic substance of a cell, comprising the steps of: designing a DNA binding protein; determining a DNA base sequence; cloning the DNA base sequence; preparing a vector carrying the DNA sequence; and introducing the vector into a cell. Miller teaches these steps, as set forth above. The options presented in claim 1, (2-1) to (2-50), recite combinations of three amino acids in the PPR motifs, and the DNA base that these PPR motifs may bind to. These options are not directed to an active method step, but rather are defining the amino acid positions in the various PPR motifs. The elected option of claim 1, (2-22), recites “when the target DNA base to which the PPR motif binds is C, the three amino acids, Number 1 AA, Number 4 AA, and Number "ii" (-2) AA, are an arbitrary amino acid, asparagine, and asparagine, respectively”. Koussevitsky and Small teach the structure of the elected PPR motifs from the GUN1 protein. The GUN1 protein as taught by Koussevitsky is identical to instant SEQ ID NO: 2, and therefore would have the structure recited in claim 1, option (2-22), which corresponds to PPR motif 5 as set forth in Table 2 of the specification, and would be expected to be capable of binding C.
Applicant argues that a DNA-binding protein generally does not bind to RNA, and an RNA-binding protein does not necessarily bind to DNA. Applicant argues that Miller teaches that linking the TALE repeat domain to the catalytic domain of FokI did not work, discouraging those skilled in the art from replacing the TALE protein of Miller with GUN1. Applicant argues that there would be no reasonable expectation of success in view of the prior art to arrive at the claimed invention.
In response to this argument, it is noted that while Miller teaches that simply linking the TALE repeat domain to the catalytic domain of FokI may not be effective, Miller successfully utilizes a different approach, wherein TALE truncation variants are linked to the catalytic domain of FokI, (Miller pg. 147 “Discussion”). Miller teaches that the designed TALEs bind DNA, and that the TALE constructs are used effectively in a method of modifying the genetic substance of a cell (Miller “Abstract”; pg. 147 “Discussion”). This meets the requirements of the instantly claimed method, as set forth above. Further, Koussevitsky teaches that the GUN1 protein comprising PPR motifs binds DNA in addition to RNA and has distinct function than other PPR proteins, as discussed above (Koussevitsky pg. 715 col. 3). Therefore, a skilled artisan would not be discouraged from replacing the TALE protein of Miller with GUN1, and could expect success as the method taught by Miller using a plant DNA binding protein is effective for gene editing, and GUN1 PPR motifs are known to bind DNA and are used in nucleic acid editing as taught by Koussevitsky.
Double Patenting
The provisional rejection of claims 1-5 on the grounds of nonstatutory double patenting is maintained, as set forth above.
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 EMILY F EIX whose telephone number is (571)270-0808. The examiner can normally be reached M-F 8am-5pm ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/EMILY F EIX/Examiner, Art Unit 1653
/JENNIFER M.H. TICHY/Primary Examiner, Art Unit 1653