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 .
Claim Status
Claims 1-19 are pending under examination.
Priority
The instant application claims priority to the provisional application 63/532,229, filed on 8/11/2023. The priority date of 8/11/2023 is acknowledged.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
The Information Disclosure Statements filed on 5/20/2025 (two on this date) are under consideration. Any strikethrough is owed to a lack of a copy of the document in the file wrapper.
Claim Objections
Claims 5-6 and 8-12 are objected to because of the following informalities: it is suggested, but not required, that Applicant amend each recitation of “the reference sequence” to “the reference polypeptide” for improved clarity and consistency with what is recited in claim 1. Appropriate correction is required.
Claim Interpretation
Claim 1 recites “a polypeptide comprising an amino acid sequence … selected from the group consisting of SEQ ID NO: 1-52” (emphasis added). This claim is being interpreted as a peptide or protein encompassing or containing the entirety of one of SEQ ID NO: 1-52 meets the limitation of the claim. Conversely, smaller fragments encompassed by SEQ ID NO: 1-52 (i.e., dipeptides) are being interpreted as not meeting the limitations of the claim. The recitation of “an amino acid sequence” in claims 2-4 and 7 are being interpreted in the same manner.
Claim 1 further recites that the polypeptides are sequence-specific DNA-binding polypeptides, which is being interpreted as an inherent characteristic of the polypeptides imparted by their amino acid sequences.
Additionally, the claimed polypeptides are being interpreted based upon what is listed in the Sequence Listing.
Examiner’s Note
A rejection under 35 U.S.C. 112(a) for written description was considered for claims 1-19 but ultimately not rendered for the following reasons: The instant specification provides sufficient data for a person skilled in the art to be able to derive polypeptides with at least 50% sequence identity capable of binding DNA. Table 1 depicts the amino acid sequences of SEQ ID NO: 1-52, including the critical residues (bolded) and the residues that constitute the binding interface with the target DNA sequence (underlined). Tables 1 and 2 further indicate the nucleotide sequences that are recognized by each of SEQ ID NO: 1-52.
Each of SEQ ID NO: 1-52 is approximately 50 or more amino acids in length. Most binding interfaces are 15 amino acids or shorter. Thus, one skilled in the art seeking to derive a polypeptide with at least 50% sequence identity to one of SEQ ID NO: 1-52 would necessarily recognize to avoid substitutions in the binding interface, which constitutes less than 50% of the total sequence length. Further, one skilled in the art would be able to use the information included in Tables 4-19 to further modify any region of SEQ ID NO: 21-23, 25, 26, 30, 31, 34, 36, 38, 44, 49, 1, 2, 4, 15, and 50-52 as each of Tables 4-19 describe in detail the best and tolerable substitutions at each position within the peptide sequence as well as ideal insertion sites.
For these reasons, the claims have been found to meet the written description requirement of 35 U.S.C. 112(a).
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 1-19 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.
Claim 1 recites a polypeptide comprising an amino acid sequence at least 50% identical, not including any amino acid insertions at identified insertion sites (i.e., any insertions are not considered when determining percent identity to the reference polypeptide), to the amino acid sequence selected from the group consisting of SEQ ID NO: 1-52, wherein the polypeptide is a sequence-specific DNA-binding polypeptide. The scope of this claim is indefinite for three reasons.
The first reason is that SEQ ID NO: 1-52, as listed in the Sequence Listing, do not indicate any amino acid insertions or insertion sites. Consequently, it is unclear what the limitation “not including any amino acid insertions at identified insertion sites” refers to.
The second reason is that it is unclear whether what is recited in the parentheses “(i.e., any insertions are not considered when determining percent identity to the reference polypeptide)” is part of the scope of the claim.
The third reason is the phrase of “i.e.,” renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
For purposes of examination, the claim is being interpreted as a polypeptide comprising at least 50% identity to any one of SEQ ID NO: 1-52 as listed in the Sequence Listing meets the limitations of the claim.
Further, by virtue of their dependency on claim 1, claims 2-19 are also hereby rejected for this same reasoning.
Claim 5 is further rejected as being indefinite for two reasons.
The first reason is that the claim recites the polypeptide of claim 1 wherein the residues in bold font are conserved (i.e., identical relative to the reference sequence). The polypeptides listed in the Sequence Listing do not possess any bolded residues; thus, this limitation renders the scope of claim 5 indefinite.
The second reason is the phrase of “i.e.,” renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Additionally, claim 6 recites the polypeptide of claim 1 wherein underlined residues are conserved relative to the reference sequence. The polypeptides listed in the Sequence Listing do not possess any underlined residues; thus, this limitation renders the scope of claim 6 indefinite.
Additionally, claims 8-11 each recite limitations in reference to Tables 4-19 of the instant specification. The claim is indefinite because tables can be readily incorporated into the claim and reference to the specification is improper. Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant's convenience." Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993)." MPEP 2173.05(s).
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 7, and 15 are rejected under 35 U.S.C. 101 because they are directed to a judicial exception.
The Supreme Court has given a three-part test for patent eligibility (see flowchart of MPEP 2106(III)):
Are the claims drawn to a process, machine, manufacture, or composition of matter?
2a) If the claims pass the first test, are the claims drawn to a judicial exception (a law of nature, a natural phenomenon (product of nature), or an abstract idea)?
2b) If a judicial exception applies, do the claims recite additional elements that amount to significantly more than the judicial exception?
Applying the three-part test to the instant claims:
Regarding 1), the claims are drawn to peptides, which are compositions of matter.
Regarding 2a), the peptides claimed read on products of nature. The claims are drawn to polypeptides with at least 50% sequence identity to any one of SEQ ID NO: 1-52 and nucleic acids encoding said polypeptides. Polypeptides with at least 50% identity reads on the following naturally-occurring products:
SEQ ID NO: 7
UniProt ID A0ABY8G021_9SPHN
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162
572
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Greyscale
SEQ ID NO: 33
UniProt ID A0ABW5JJ26_9BACT
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150
584
media_image2.png
Greyscale
SEQ ID NO: 36
UniProt ID A0ABV6SKF7_AZOPA
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230
630
media_image3.png
Greyscale
UniProt ID C1DIF0_AZOVD
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media_image4.png
240
628
media_image4.png
Greyscale
UniProt ID A0ABN6MU63_9BACT
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248
638
media_image5.png
Greyscale
SEQ ID NO: 40
UniProt ID A0ABX7LHX2_9BACL
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172
650
media_image6.png
Greyscale
UniProt ID A0ABN8GSP1_9BACL
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168
630
media_image7.png
Greyscale
*Other not listed here
SEQ ID NO: 41
UniProt ID A0A928Z1E2_9CYAN
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154
622
media_image8.png
Greyscale
UniProt ID A0A2A9E752_9MICO
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172
622
media_image9.png
Greyscale
*Others not listed here
SEQ ID NO: 42
UniProt ID K1JL72_9BURK
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172
632
media_image10.png
Greyscale
UniProt ID A0A379AQP9_AVIAV
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162
628
media_image11.png
Greyscale
*Others not listed here
SEQ ID NO: 43
UniProt ID A0ABV3SFH5_9HYPH
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172
632
media_image12.png
Greyscale
UniProt ID A0A1L3SVK7_9HYPH
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150
630
media_image13.png
Greyscale
*Others not listed here
SEQ ID NO: 44
UniProt ID A0A9X3N3X7_9ACTN
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156
616
media_image14.png
Greyscale
UniProt ID A0A6H9Z2A6_9ACTN
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174
638
media_image15.png
Greyscale
*Others not listed here
SEQ ID NO: 45
UniProt ID A0ABP7AV50_9ACTN
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158
628
media_image16.png
Greyscale
UniProt ID A0A0N8GNQ2_9CHLR
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170
624
media_image17.png
Greyscale
*Others not listed here
SEQ ID NO: 46
UniProt ID A0A0D0P6Z8_KITGR
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166
626
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Greyscale
UniProt ID A0A2T4UH37_9ACTN
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168
620
media_image19.png
Greyscale
*Others not listed here
SEQ ID NO: 47
UniProt ID A0A318NIF2_9ACTN
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156
628
media_image20.png
Greyscale
UniProt ID A0A919J8S2_9ACTN
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154
620
media_image21.png
Greyscale
*Others not listed here
SEQ ID NO: 48
UniProt ID A0ABV3J1E6_9ACTN
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250
624
media_image22.png
Greyscale
UniProt ID A0ABW6U561_9ACTN
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244
636
media_image23.png
Greyscale
*Others not listed here
SEQ ID NO: 49
UniProt ID A0A668T3D8_OREAU
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162
622
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Greyscale
UniProt ID A0A669BRD4_ORENI
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174
626
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Greyscale
*Others not listed here
Regarding 2b), there is nothing significantly more recited in the claims that would distinguish the claimed polypeptides from the natural products described above; the nucleic acids encoding said polypeptides, as recited in claim 15, would also be indistinguishable from the naturally-occurring genes encoding said natural products. As such, the claims do not contain elements added to the judicial exception to render the claims significantly more than the exception.
In sum, the claims are drawn to patent ineligible subject matter and are rejected here.
Claim Rejections - 35 USC § 102
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
A polypeptide with at least 50% identity to SEQ ID NO: 1, 2, 41-43, and 47
Claim(s) 1, 7, 13, and 15-17 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Lee et al. (US20090215168A1, published 8/27/2009).
Lee teaches isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius (Abstract).
Regarding claims 1 and 7, Lee teaches SEQ ID NO: 994, which exhibits 49.6% (rounding to 50%) sequence identity to the instant SEQ ID NO: 1:
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172
630
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;
SEQ ID NO: 992, which exhibits 53.5% sequence identity to the instant SEQ ID NO: 2
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186
624
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and also exhibits
52.9% sequence identity to the instant SEQ ID NO: 41
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154
618
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Greyscale
;
SEQ ID NO: 989, which exhibits 51.7% sequence identity to the instant SEQ ID NO: 42
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176
618
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Greyscale
;
SEQ ID NO: 1877, which exhibits 52.7% sequence identity to the instant SEQ ID NO: 43
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186
626
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Greyscale
; and
SEQ ID NO: 993, which exhibits 55.7% sequence identity to the instant SEQ ID NO: 47
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188
634
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(Sequence Listing).
Regarding claim 13, Lee teaches variants of the invention may consist of producing a recombinant polypeptide fused to a carrier protein (chimeric protein; fusion protein; [0267]).
Regarding claims 15-17, Lee teaches nucleic acids, expression vectors, and host cells expressing said vectors of the invention; the vector may contain a promoter ([0252-0253]).
A polypeptide with at least 50% identity to SEQ ID NO: 44, 46, and 48
Claim(s) 1, 7, 13, and 15-17 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Pompejus et al. (US20050153402A1, published 7/14/2005).
Pompejus teaches isolated nucleic acid molecules, designated MR nucleic acid molecules, which encode novel MR proteins from Corynebacterium glutamicum. The invention also contemplates recombinant expression vectors containing MR nucleic acid molecules, and host cells into which the expression vectors have been introduced as well as fusion proteins (Abstract).
Regarding claims 1 and 7, Pompejus teaches SEQ ID NO: 142, which exhibits 54.3% sequence identity to the instant SEQ ID NO: 44
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162
628
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Greyscale
50.7% sequence identity to the instant SEQ ID NO: 46
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170
620
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; and
49.5% (rounding to 50%) sequence identity to the instant SEQ ID NO: 48
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164
630
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(Sequence Listing).
Regarding claim 13, Pompejus teaches fusion proteins (Abstract).
Regarding claims 15-17, Pompejus teaches nucleic acids, expression vectors encoding said nucleic acids, and host cells encoding said expression vectors (Abstract). The expression vectors can comprise promoters ([0081]).
A polypeptide with at least 50% identity to SEQ ID NO: 45
Claim(s) 1 and 15 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Selber (US20130302855A1, published 11/14/2013).
Selber teaches the DNA-sequence of the wild type genome of Actinoplanes utahensis as well as all genetic modifications introduced into the wild type-and further developed strains (Abstract; [0001]).
Regarding claim 1, Selber teaches SEQ ID NO: 15314, which exhibits 49.5% (rounding to 50%) sequence identity to the instant SEQ ID NO: 45
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156
636
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(Sequence Listing).
Regarding claim 15, as stated above, Selber teaches DNA-sequences of the invention (nucleic acid encoding said polypeptide; Abstract).
A polypeptide with at least 50% identity to SEQ ID NO: 49
Claim(s) 1, 7, 13, and 15-17 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Murray et al. (US20030105002A1, published 6/5/2003).
Murray teaches the invention relates to the discovery of novel genes encoding RGS polypeptides. Therapeutics, diagnostics and screening assays based on these, molecules are also disclosed (Abstract).
Regarding claims 1 and 7, Murray teaches SEQ ID NO: 25, which exhibits 54.6% sequence identity to the instant SEQ ID NO: 49
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170
642
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(Sequence Listing).
Regarding claim 13, Murray teaches chimeric molecules (e.g., fusion proteins) ([0014]).
Regarding claim 15, Murray teaches nucleic acids of the invention (see, for instance, [0007]).
Regarding claims 16 and 17, Murray further teaches expression vectors further comprising a promoter as well as host cells comprising the expression vector ([0010]).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sara Konopelski Snavely whose telephone number is (571)272-1841. The examiner can normally be reached Monday - Friday 9-6pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Melissa L Fisher can be reached at 571-270-7430. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SARA E KONOPELSKI SNAVELY/Examiner, Art Unit 1658
/Melissa L Fisher/Supervisory Patent Examiner, Art Unit 1658
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