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 .
Application Status and Election
Claims 1-7 and 9-11 are pending.
Applicant’s election without traverse of Group I, in the reply filed on August 25, 2025 is acknowledged. Claims 2, 4-5 and 9 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant does point out that claim 2 comprises one or more inverted promoters (page 7, ¶3). However, the groups are still distinct because the inverted promoter drives expression of the first coding sequence in between the two recombinase sites even when inverted with respect to the first promoter. Therefore, the DNA elements of claims 1 and 2 are distinct, with expression of coding sequences either contingent or not contingent upon inversion.
Claims 1, 3, 6-7 and 10-11 are under examination.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency #1 – Nucleotide sequences appearing in the drawings in FIG. 15 are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. The nucleotide sequences in FIG. 15 appear to be SEQ ID NOs 81 and 82.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers (noted above);
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The use of the terms CutSmart®, QiaQiuck®, EpMotion®, QiaPrep®, OptiMEM®, and Nucleofector®, which are trade names or marks used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 10 and 11 are objected to because of the following informalities:
Claim10 recites “in the generation of a recombinase recognition sequence between the first promoter and the first gene following recombination…” It is clear that “the first gene” is referring back to “the first open reading frame”. However, for consistency it is suggested that “the first gene” in line 10 be changed to “the first open reading frame”.
Claim 11 depends from claims 2 and 7, which are withdrawn claims. Claim 11 is objected to for depending from a withdrawn claim. To remedy the objection, it is suggested to remove references to claim 2 and 7.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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 3, 6, 7, 10, and 11 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 3 recites two DNA element options (a) and (b), which differ slightly in the coding sequence.
Claim 3, part (a) is indefinite because it recites “a coding sequence, which encodes either exclusively the Rep78 protein or exclusively the Rep68 protein, but not both, wherein (i) optionally the internal P40 promoter is inactivated, and/or (ii) the start codon of Rep52/40 is mutated… and/or (iii) splice donor and acceptor sites are removed, which is inverted with respect to the coding strand, and which is operably linked to the…” Due to the combination of “optionally” within (i), and two recitations of “and/or” between options (ii) and (iii), it is not clear which, if any of (i), (ii) or (iii) are needed. It is clear that option (i) is optional. But it is not clear if the “optionally” should extend to items (ii) and (iii) such that none of those options are required, or alternatively if at least (ii) or (iii) is needed.
Claim 3, part (a) is also indefinite because “the Rep78 protein” and “the Rep68 protein” lack clear antecedent basis. Rep78 and Rep68 proteins encompass a genus of proteins including native Rep78 and Rep68 proteins from different AAV species and protein variants of the native Rep78 and Rep68 proteins. A brief search of possible Rep68 and Rep78 proteins in Genbank found proteins of different lengths depending on whether the proteins were derived from human, bat or avian AAV strains. As such it is not clear what protein structures “the Rep78 protein” and “the Rep68 protein” are referring to. It is suggested that “the” be replaced with “a”.
Claim 3, part (b) recites “a coding sequence, which encodes either exclusively the Rep78 protein or exclusively the Rep68 proteins, but not both, wherein (i) optionally the internal promoter is inactivated…, and/or (ii) the start codon of Rep52/40 is mutated… and (iii) splice donor and acceptor sites are removed, which is inverted with respect to the coding strand, and which is operably linked to the…” Claim 3, part (b) is indefinite due to the combination of “optionally” within (i), with one recitation of “and/or” and one recitation of “and” between options (ii) and (iii), it is not clear which, if any, of (i), (ii) or (iii) are needed. It is clear that option (i) is optional. But it is not clear if the “optionally” should extend to items (ii) and (iii) such that none of those options are required, or alternatively if at least (ii) or (iii) is needed. Additionally, the combination of “and/or” and “and” makes it unclear whether if (ii) is included, then (iii) must also be included.
Claim 3, part (b) is also indefinite because “the Rep78 protein” and “the Rep68 protein” lack clear antecedent basis for the reasons explained above in paragraph 16.
Claim 3, part (b) is also indefinite because “the internal promoter” lacks clear antecedent basis. Bennett teaches that the Rep78 and Rep68 coding sequences comprise at least two internal promoters: the p19 promoter and the p40 promoter (Bennett et al., Future Virol. (2017), 12: 283-297; Fig 1). It is not clear which internal promoter “the internal promoter” is referring to.
Claim 3, part (b) also recites “The Rep52 open reading frame… or the Rep40 open reading frame… including a polyadenylation signal operably linked to said open reading frame.” This phrase renders the claim indefinite because “the Rep52 open reading frame” and “the Rep40 open reading frame” lack clear antecedent basis. The Rep52 and Rep40 open reading frames (ORFs) encompass a genus of ORFs including native ORFs from different AAV species and additionally ORFs that have been altered, such as to remove splice sites. A brief search of possible Rep52 and Rep40 ORFs in Genbank found ORFs of different lengths and sequences depending on whether the ORFs were derived from human, bat or avian AAV strains. As such it is not clear what nucleic acid structures “the Rep52 open reading frame” and “Rep40 open reading frame” are referring to. Furthermore, it is not clear which ORF “said open reading frame” is referring to.
Due to the similarities between claim 1, claim 3-part (a), and claim 3-part (b), to remedy the indefiniteness, it is suggested to make claim 3-part (a) and claim 3-part (b) into two different dependent claims that depend from claim 1. Suggested claim language:
Part (a): Claim X. The double stranded DNA element of claim 1, wherein the first open reading frame encodes either exclusively a Rep78 protein or exclusively a Rep68 protein, and wherein the second open reading frame is a Rep52/Rep40 and Cap open reading frames.
It is suggested that the optional items be included in a further dependent claim.
Part (b): Claim X. The double stranded DNA element of claim 1, wherein the first open reading frame encodes either exclusively a Rep78 protein or exclusively a Rep68 protein, and wherein the second open reading frame is a Rep52 open reading frame or a Cap open reading frame, optionally wherein the splice donor and acceptor sites of the Rep52 open reading frame are removed.
Claim 6 recites “The double stranded DNA element according to claim 3, where in c), the coding strand further comprises…” Claim 6 is indefinite for depending from claim 3 and not remedying the indefiniteness. Additionally, claim 3 does not recite a part (c). It is not clear if the limitations of claim 6 are to be added to claim 3, part (a) or part (b) or some other unrecited part (c). Additionally, claim 3 already recites a cap open reading frame as an option for the second open reading frame in part (a). It is unclear if the cap ORF would only be added to part (a) if the Rep52/40 ORFs were chosen.
Claim 7 recites “A double stranded DNA molecule comprising (a) the E1A open reading frame and the E1B open reading frame and/or (b) the E2A open reading frame and the E4orf6 open reading frame; characterized in that the first and second ORF of (a) or/and (b) are contained in a double stranded DNA element comprising a coding strand and a template strand…. the first open reading frame of (a) or (b) that is inverted with respect to the coding strand… the second open reading frame of (a) or (b).” The combination of two different ORFs in each of (a) and (b), with the combinations of “and/or” and “or/and” in the phrases referring to them is confusing such that it is not clear the minimum Ad ORFs that are required and in which combinations. Additionally, “the E1A open reading frame”, “the E1B open reading frame”, “the E2A open reading frame” and “the E4orf6 open reading frame” lack clear antecedent basis. The E1A, E2A, E1B and E4orf6 ORFs encompass a genus of ORFs including native ORFs from different Adenovirus species and additionally ORFs that have been altered or engineered. A brief search of possible E1A ORFs in Genbank found ORFs of different lengths and sequences depending on the strain. As such it is not clear what nucleic acids sequecnes the E1A open reading frame”, “the E1B open reading frame”, “the E2A open reading frame” and “the E4orf6 open reading frame” are referring to.
Due to the similarities between claims 1 and 7, to remedy the indefiniteness, it is suggested to make claim 7 depend from claim 1 and claim the two different ORF combinations in separate claims. Suggested claim language:
Claim X. The double stranded DNA element of claim 1, wherein the first open reading frame comprises an E1A open frame and an E1B open reading frame, and wherein the second open reading frame comprises an E2A open reading frame and an E4orf6 open reading frame.
Claim X. The double stranded DNA element of claim 1, wherein the first open reading frame comprises an E2A open reading frame and an E4orf6 open reading frame, and wherein the second open reading frame comprises an E1A open frame and an E1B open reading frame.
Claim 10 recites “the double stranded DNA element or the double stranded DNA according to claim 1, whereby the incubation of the double stranded DNA element or molecule…” Claim 1 does not recite “a double stranded DNA” or a “molecule” separate from the double stranded DNA element that is also referred to in claim 10. It is not clear what “the double stranded DNA” or “the double stranded DNA molecule” is referring to if not to the already referenced element.
To remedy the indefinites, it is suggested to delete the bolded words in the cited portion of claim 10 above.
Claim 11 recites “A mammalian cell comprising… one or more double stranded DNAs according to claim 8”. Claim 11 is rejected as being incomplete because it depends directly from a canceled base claim. To remedy the objection, it is suggested to remove references to claim 8.
Allowable Subject Matter
Claim 1 is allowed.
The following is a statement of reasons for the indication of allowable subject matter:
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Claim 1 is directed to a double strand DNA molecule comprising eight genetic elements arranged in a specific order: a first promoter (P1), a first recombinase recognition sequence (RRS1), a second promoter (P2) that drives expression on the opposite strand and in the opposite direction of the coding strand (i.e., P2 is inverted with respect to the coding strand); a first polyA or termination sequence (T1) that functions on the template strand; a first open reading frame (ORF1) that is inverted with respect to the coding strand; a second recombinase recognition sequence (RRS2); a second open reading frame (ORF2); a second polyA or termination sequence (T2). Based on FIG. 1 of the Specification, P1 and ORF2 are interpreted as NOT being inverted relative to the coding sequence. Thus, P2, T1 and ORF2 are inverted relative to P1. The claimed arrangement of the 8 elements is below. Claims 3, 6 and 7 have the same arrangement of elements and further specify that ORF1 and ORF2 are genes encoding either AAV rep and cap proteins or Adenovirus E1A/E1B and E2B/E4orf6 genes. The function of the claimed genetic arrangement is to simultaneously activate expression of ORF1 and ORF2 by treating the DNA with a recombinase enzyme that results in the inversion of the elements between RRS1 and RRS2 such that P1 becomes operably linked to ORF1-T1 and P2 becomes operably linked to ORF2-T2.
The closest prior art is Burstein (WO 9827207 A1, cited in the PCT Written Opinion of related PCT/EP2021/078268 Application). Burstein teaches activating expression of the Rep78 gene using three means: 1) Inversion of a single promoter by recombination so that it becomes operably linked to the rep78 coding sequence (Example 6, page 491); 2) Inversion of the rep78-polyA cassette by recombination so that an upstream promoter becomes operably linked to the rep78 coding sequence (Example 7, page 51); and 3) excision of a terminator by recombination so that an upstream promoter becomes operably linked to the rep78 coding sequence (Example 8, page 52). In the “flipping/inverting” examples 6 and 7, the flipped components are either a promoter or a coding sequence and terminator sequence, not all three. Burstein does not teach 1) flipping/inverting three different components at once, or 2) activating two different ORFs simultaneously by inversion.
Various DNA rearrangements using recombinases, like the Cre and Flp recombinases, are well- known in the art. See e.g., Thomson and Blechl, Recombinase technology for precise genome engineering. Advances in new technology for targeted modification of plant genomes, (2015), 113-144. Nearly all the prior art uses recombinase-mediated inversion/rearrangement in the manners disclosed in Burstein, namely excision of a stopping/terminating sequence, inversion of a single promoter, or inversion of a single coding sequence. Ungrin also teaches the simultaneous gene expression activation and repression by flipping two promoter-less open reading frames using the Cre recombination (Ungrin et al., BMC Biotechnology (2006), 6(10): 1-9; Figure 1). Examiner could not find any prior art that teaches using recombinase-mediated inversion to simultaneously activate expression of two different open reading frames. Examiner also could not find the claimed arrangement of P2, polyA, and ORF1 in between the RRSs. In the claimed arrangement, P2 does not drive expression of ORF1. Because there is no teaching in the prior art that recombinase-mediated inversion could be used for simultaneous dual gene activation, there was no motivation to combine Examples 6 and 7 in Burstein. Additionally, because there is no teaching in the art to arrange in order a promoter--terminator sequence--ORF (reference to template) or ORF-terminator-promoter (reference to coding sequence) such that they are not operably linked to each other prior to rearrangement, there was no reason to modify the genetic rearrangements in Burstein as such.
Regarding subject matter eligibility under 35 USC § 101, the claims recite a double stranded DNA element/molecule, which potentially could be a product of nature. However, the claimed DNA element is markedly different than its closest naturally occurring counterpart, a bacterial gene cluster comprising coding regions, promoters and terminators flanked in various ways by recombinase recognition sequences. Trzilova teaches that bacterial genomes normally undergo site-specific recombination to produce complex phenotypic heterogeneity in populations (Trzilova and Tamayo, Trends in Genetics (2019), 37: 59-72; Abstract). Trzilova teaches one such bacterial gene cluster that comprises a promoter flanked by RRSs, or several ORFs flanked by RRSs, either of which can be flipped to operably drive expression of different sets of ORFs (Figure 2). However, it appears that the bacterial gene clusters comprise a single promoter, which differs from the claimed DNA element that requires two promoters that are both operably linked to ORFs upon inversion. Additionally, the claimed RRSs require “a mutation in the left [or right] inverted repeat”. This mutation limits the number to times the RRSs can be recombined to a single recombination/inversion event. There is no evidence in the art that bacterial recombinase sites have a sequence that only allows a single recombination event. Therefore, the claimed DNA element with mutated RRSs and multiple promoters oriented in opposite orientation from each other is markedly different than the naturally occurring counterpart. The claims are directed to eligible subject matter at Step 2A, prong 1 of the Subject Matter Eligibility Test.
Conclusion
Claim 1 is allowed. Claims 10-11 are objected to. Claims 3, 6-7, 10-11 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHERINE KONOPKA whose telephone number is (571)272-0330. The examiner can normally be reached Mon - Fri 7- 4.
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/CATHERINE KONOPKA/Examiner, Art Unit 1635