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 .
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 11/06/2025 has been entered.
Claims 1 and 4-14 are currently pending. Applicant has amended claims 1, 4 and 7, added claim 14, and cancelled claims 2-3 by amendment filed on 11/06/2025. Claims 9-13 were previously withdrawn from consideration pursuant to 37 CPR 1.142(b) as being drawn to a nonelected subject matter, there being no allowable generic or linking claim.
Therefore, claims 1, 4-8, and 14 are currently under examination to which the following grounds of rejection are applicable.
Priority
The instant application is a national stage entry under 35 USC 371 of PCT/JP2020/015966 (filed 04/09/2020), which claims benefit of foreign application JAPAN 2019-074004 (filed 04/09/2019).
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed on 10/04/2021.
Withdrawn objections/ Rejections
Claim Rejections - 35 USC § 102
In view of Applicants’ amendment, the rejection of claims 1 and 6 under 35 USC § 102 as being anticipated by Rinaldi et al. (Rinaldi et al., Nucleic Acids Res. 2017, of record) has been withdrawn.
A response to Applicant’s arguments with regard to a withdrawn rejection is moot except where relevant to the modified rejection of claims 1 and 6.
Maintained and modified rejections in response to Applicants’ arguments or amendments
Claim Rejections - 35 USC § 112(b)
Claims 1 and 4-8 remain 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.
Note: The rejection is modified for consideration of the amendments filed 11/06/2025. Claim 1 remains indefinite. It is unclear what the intended structure is with respect to the phrase “an RVD sequence of the TAL-repeats is histidine-threonine, arginine-serine,
or histidine-serine.”, therefore the claim as written is indefinite. Does this recitation mean two consecutive amino acids in the 5’—3’ direction? As such the metes and bounds of the claim are indefinite. Claims 4-8 and 14 are dependent upon and inherit the deficiencies of claim 1.
Claim 4 remains indefinite in its recitation of “same amino acid sequence” . Claim 1 (from which claim 4 depends) recites multiple TAL-repeats , however claim 1 requires 1 RVD sequence of the TAL-repeats is histidine-threonine, arginine-serine, or histidine-serine. Therefore, it is unclear to what “same amino acid sequence” is referring to as a TAL-repeat may contain RVDs with no co-occurring identical RVDs. As such the metes and bounds of the claim are indefinite.
Claim 7 remains rejected because of its recitation of “protein containing the DNA-binding domain and a fluorescent protein are directly or indirectly bound to each other” because it is unclear if the claimed nucleic acid-binding protein essentially consisting of “a DNA-binding domain in which 3 or more and less than 35 TAL-repeats are repeatedly linked” further comprises a protein and a fluorescent protein or the phrase “ protein containing the DNA-binding domain” refers to “ a DNA-binding domain” of the nucleic acid-binding protein. A such the metes and bounds of the claim are indefinite.
For the sake of compact prosecution, the examiner is interpreting claim 7 as a protein containing a DNA-binding domain which is bound to a fluorescent protein.
Claim Rejections - 35 USC § 103
Claims 1, 6 and 14 are newly rejected and claims 4-5 remain rejected under 35 U.S.C. 103 as being unpatentable over Rinaldi et al. (Rinaldi et al., Nucleic Acids Res. 2017, of record) in view of Shi et al. (CN103319574, of record).
Note: The rejection is modified for consideration of the amendments filed 11/06/2025.
Regarding Claims 1 and 14, Rinaldi teaches both naturally occurring and synthetically designed DNA binding proteins, TAL (Transcription Activator-Like) Effector (TALE), TALEs, binding to non-target sequences on DNA. Rinaldi further teaches determination of the TALEs target DNA affinity versus non-target DNA affinity using TALE with up to 25 repeats (which anticipates the range of 3-35 repeats “This revealed that even with different hypothetical RVD compositions, TALEs reach an optimum length for specificity, between 16 and 25 repeats for the variations we modeled”, (Pg. 6961, final paragraph of Introduction). Rinaldi also teaches that an increase to the number of Repeat Variable Di-residue (RVD) sequences increases the affinity for NON-target DNA (Pg. 6966, 3rd paragraph and Figure. 4). Furthermore, Rinaldi discloses “The difference between the effect of length on affinity for target versus nontarget DNA manifests in specificity increasing then diminishing with increasing TALE length, peaking between 15 and 19 repeats.” (Abstract). This falls within the range of the newly added instant claim 14, which recites: “…the repetition number of the TAL-repeats in the DNA-binding domain is 3 or more and less than 15.”
Rinaldi et. al does not teach the incorporation of an RVD sequence of the TAL-repeats is HT (Histidine-Threonine), RS (Arginine-Serine), or HS (Histidine-Serine) in instant claims 1 and 5. Rinaldi et al. does not teach the that the nucleic acid binding protein wherein in the DNA binding domain, the TAL-repeats consisting of the same amino acid sequence are linked repeatedly for instant claim 4.
Shi et al. cures the deficiencies of Rinaldi as they teach an amino acid sequence for a DNA binding domain and TAL, LTPDQVVAIA ASX1X2GGKQALETVQRLLPVLCQAHG, in which the X1X2 (RVD) were the sequence is selected from a group that includes HT and HS and that the inclusion of these alternative bases alters the base-recognition characteristics of the RVD (Pg. 2, under Description, Disclosure of Invention Section). Further Shi et al. teach the sequence described above, linked repeatedly to include 10 repeats (claim 1 of Shi et al.). These repeats can include the HT and/or HS sequence described above and could thus result in a repeat of the same sequences repeatedly if either HT or HS was chosen as the X1X2 variable.
It would have been obvious to a person of ordinary skill in the art, at the time of the invention to have modified the DNA-binding proteins (TALEs) taught by Rinaldi et al. to further include the amino acid sequence for a binding domain and TAL that includes HT or HS as an RVD sequence and in the additional TAL- linked repeats, because the alternative bases and repeats would serve to alter the base-recognition capacity of the DNA binding proteins. Moreover, it would have been obvious to one of ordinary skill in the art that Rinaldi et al.’s teachings of DNA binding protein affinities to DNA base pairs, would have been modified by the inclusion of non-canonical RVDs such as HT or HS with the expectation of further characterizing how both TAL repeat size, and specific RVD sequence effect the binding affinity. There would be reasonable expectation of success in combining these methods, as both Rinaldi and Shi teach DNA base binding affinities of TAL-repeats having RVDs that specifically recognize a specific nucleobase and the role played by the composition of the binding domains.
Regarding Claim 6, Rinaldi teaches sequences derived from naturally occurring Xanthomonas TALES that have been genetically engineered to incorporate increased numbers of repeats. This modification altering the naturally occurring TALE is analogous to an engineered amino acid mutation (amino acid addition/insertion to alter the sequence and corresponding binding) (Pg. 2017, Right Column, 1st Paragraph).
Claims 7 and 8 remain rejected under 35 U.S.C. 103 as being unpatentable over Rinaldi et al. (Rinaldi et al., Nucleic Acids Res. 2017) in view of Shi et al. (CN103319574) as applied to claim 1 above and further in view of Lopes Novo et al. (Lopes Novo C, Brief Funct Genomics. 2016).
Regarding claim 1, Rinaldi and Shi render obvious claim 1, as iterated above in the 103 rejection, the content of which is incorporated herein, in its entirety.
Rinaldi et al. and Shi et al. do not teach a protein containing a DNA-binding domain which is bound to a fluorescent protein. Additionally, Rinaldi et al. and Shi et al. do not teach a protein probe comprising the nucleic acid-binding protein according to claim 1.
Lopes Novo et al. teaches a protein probe bound to a TALE, specifically they teach “ systems that enable live imaging of nuclear organization and sub-nuclear compartments in individual cells, which is attractive for studying dynamic processes such as the cell cycle and chromatin structure. Endogenous repetitive genomic sequences, including centromeres, telomeres and pericentric heterochromatin, can be visualized through sequence-specific TALEs fused to monomeric green fluorescent protein (GFP) ( Figure 2A)”. The teaching of Lopes Novo further underscores the utility of this combination as they teach that “The TALE approaches (TALE combined with a protein probe) open up an exciting new area of cell biology, enabling real-time experiments to track the movement of chromatin and specific DNA regions, as well as imaging through cell division and other cell processes (Pg. 8, Paragraph 4). This renders obvious claim 7 encompassing a DNA binding protein bound to a fluorescent protein (GFP-fluorescent protein) and further this entire structure (TALE+GFP) renders obvious a protein probe comprising the nucleic acid binding protein of claim 1.
Within claim 8, “which selectively binds to an open chromatin structure” is intended use and does not serve to further limit the claim, which is for a protein probe comprising the nucleic acid binding protein according to claim 1. The prior art structure (TALE) taught by Rinaldi et al. as modified by the teaching of Shi et al. and Lopes Novo et al. would be indistinguishable from the instant application claims and thus capable of performing the recited intended use, therefore this limitation is met. See e.g. In re Schreiber, 128 F.3d 1473, 1477; 44 USPQ2d 1429, 1431 (Fed. Cir. 1997); MPEP 2114 (Apparatus Claims Must Be Structurally Distinguishable From the Prior Art).
It would have been obvious to a person of ordinary skill in the art, at the time of the invention to have further modified the DNA-binding proteins (TALEs) taught by Rinaldi et al. and Shi et al. to further include the use of a GFP fluorescent protein, because this would allow for the TALE to function as a probe for the use of visualization and quantification of live imaging of nuclear organization and sub-nuclear compartments in individual cells . There would have been reasonable expectations of success in combining these teachings as one of ordinary skill in the art would recognize to combine known elements in the art to give predictable results.
Response to Applicants’ Arguments as they apply to the rejection of claims 1 and 14 newly rejected under 35 U.S.C. 103 and claims 4-8 which remain rejected under 35 U.S.C. 103
At pages 7 of the remarks filed on 11/06/2025, Applicants essentially argue “In all of Rinaldi, Shi, and Lopes Novo, RVDs are used to bind to specific base sequences. In Shi, HT, RS, and HS are also disclosed as RVDs that specifically bind to particular bases (Table 1). While these references suggest that using RVDs with low base specificity (RVDs that bind to all four bases with equal strength in some of the TAL repeat units would reduce specificity to the target base sequence and allow binding to base sequences similar to the target sequence, it is not obvious that a TALE composed solely of RVDs with low base specificity would be able to bind nucleic acids in the base sequence-independent manner. Rinaldi states that "decreasing specificity by increasing the number of repetitions" is a problem that needs to be solved. There is therefore no motivation to substitute the RVD sequences such as HT and HS described by Shi in order to achieve a problem equivalent to this one. Therefore, Rinaldi in view of Shi, and/or Lopes Novo, alone or in combination, cannot render amended claim 1 obvious.” Moreover, at pg. 6 applicant argues that the phrase "the specificity is decreased" mentioned in Rinaldi means that the specificity for a specific target base sequence is reduced and binding to base sequences similar to the target base sequence is increased. This does not mean that it binds to all nucleic acids regardless of their base sequence. Thus, in Rinaldi, "decreasing specificity by increasing the number of repetitions" means that the probe will bind not only to the target base sequence but also to base sequences similar to that base sequence. This is different from "the base sequence-independent manner" of the present invention, which means binding to all nucleic acids regardless of the base sequence.
Applicant’s arguments have been considered but have not been found persuasive.
Claim 1 recites, “A nucleic acid-binding protein essentially consisting of a DNA-binding domain in which 3 or more and less than 35 TAL-repeats are repeatedly linked, wherein an RVD sequence of the TAL-repeats is histidine-threonine, arginine serine, or histidine-serine.”
As written the claim does not require all RVDs to be composed of histidine-threonine, arginine serine, or histidine-serine or sequence independent binding. A repeat of histidine-threonine, arginine serine, or histidine-serine is explicitly disclosed in Shi. As the combination of Rinaldi et al. and Shi et al. render obvious for an RVD sequence of the TAL-repeats to include HT or HS because the alternative bases and repeats would serve to alter the base-recognition capacity of the DNA binding proteins, in contrast to Applicant’s arguments where “binding to all nucleic acids regardless of the base sequence” would have been reasonably expected as the structure of the claimed RVD sequence of the TAL-repeats being is histidine-threonine, arginine serine or histidine-serine and the structure rendered obvious by Rinaldi and Shi are the same.
Further, the teachings of Rinaldi do not exclude or teach away from the use of the RVDs taught by Shi. Teaching away requires the prior art to criticize, discredit, or otherwise discourage the claimed solution, from MPEP § 2141.02(VI): “the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed.” Moreover, Rinaldi does teach modifying repeats to more fully characterize specificity. Rinaldi does not teach that low-specificity RVDs are wholly inoperable. Since the prior art clearly does not do this, applicants’ argument that “Rinaldi states that "decreasing specificity by increasing the number of repetitions" is a problem that needs to be solved. There is therefore no motivation to substitute the RVD sequences such as HT and HS described by Shi in order to achieve a problem equivalent to this one...” is unconvincing.
New claim objection/rejections
Claim 4 is objected to because of the following informalities: abbreviations such as RVD should be spelled out at the first encounter in the claims. Appropriate correction is required
Claim 4 is objected to because it is missing an indefinite article preceding the term “same amino acid” . It should be corrected to recite “a same amino acid”. Appropriate correction is requested.
Claim 4 is grammatically incorrect in its recitation of “amino acid sequence are liked “ . The third singular form in present of the verb “to be” should be used rather than the plural form. The claim should be corrected to recite “amino acid sequence is linked repeatedly”. Appropriate correction is requested.
35 U.S.C. 112(d):
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.
Claim 5 is 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. This is a new rejection necessitated by Applicant’s amendments to the claims filed on 11/07/2025. Claim 5 depends from claim 1. Claim 1 newly requires that an RVD sequence of the TAL-repeats is histidine-threonine, arginine serine,
or histidine-serine. Claim 5 does not limit the scope of the claimed RVD sequence, permitting that it may be “modified to histidine-threonine, arginine-serine, or histidine-serine.”
Applicant may cancel the claim, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Conclusion
Claims 1, 4-8 and 14 are rejected. No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KODYE LEE ABBOTT whose telephone number is (703)756-1111. The examiner can normally be reached M-F 8-5.
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/KODYE LEE ABBOTT/Examiner, Art Unit 1634
/MARIA G LEAVITT/Supervisory Patent Examiner, Art Unit 1634