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 the Claims
Claim 1 is pending. Claim 1 is the subject of this NON-FINAL Office Action. This is the first action on the merits.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. Please note that the certified copy was uploaded in reverse page order.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on pg. 61, line 19; pg. 73, line 30; and pg. 78, line 8.
Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1 contains the terms “RTtag” and “RTprimer.” The abbreviation “RT” should be spelled out in full the first time the term appears in the claim e.g. reverse transcription tag (RTtag) and reverse transcription primer (RTprimer).
Claim 1, line 6 and line 13 end in periods. Periods are only to be used at the end of the claim; periods may not be used elsewhere in the claims except for abbreviations. See MPEP 608.01(m).
Appropriate correction is required.
Claim Interpretation
Claim 1 recites the limitation “gene L.” Pg. 18 states that “[t]he ‘selected gene’ or ‘gene of interest’ (gene L) of the tpRNA refers to a sequence of any protein or nucleic acid of interest that should be submitted to the targeted molecular evolution approach of the invention.” The limitation “gene L” will be interpreted as encompassing any protein or nucleic acid.
Claim 1 recites the limitation “a scaffold protein.” Pg. 20 of the specification states that “a ‘scaffold protein’ (SP) refers to a protein expressed by the bacterial cell and capable of binding both to the SPBM1 of the tpRNA via a first specific biding site (SPS1) and to the SPBM2 of the prRNA via a second binding site (SPS2). The scaffold protein will be interpreted as any protein expressed by the bacterial cell, where the protein must be capable of binding both to the SPBM1 of the tpRNA via a first specific biding site (SPS1) and to the SPBM2 of the prRNA via a second binding site (SPS2). Under the broadest reasonable interpretation, the scaffold protein is not required to be bound to the SPBM1 and/or the SPBM2, but must only have the ability to bind to these regions.
Claim 1 recites the limitation “an RTtag sequence operably linked to the gene L.” Pg. 18 of the specification states that “[t]he ‘RTtag’ of the tpRNA refers to an oligoribonucleotide sequence corresponding to the substantially complementary sequence of a another oligoribonucleotide that functions as a primer for reverse transcription (RTprimer). The RTtag sequence will be interpreted as a sequence complementary to a reverse transcription primer.
Claim 1 recites the limitation “a fusion protein (RBD-RT) comprising a reverse transcriptase (RT) and an RBM binding domain (RBD) capable of binding to the RBM of the prRNA.” Pg. 19 of the specification states “[t]he reverse transcriptase domain (RT), optionally of the RBD-RT, refers to an error-prone RT, i.e. an enzyme capable of generating altered copies of cDNA from an RNA template. Accordingly, the role of the RT used in the methods of the disclosure is to generate altered cDNA copies from the gene L sequence of the tpRNA. Besides, as the error rate of any RT is theoretically > 0, it follows that any RT is an error-prone RT and is therefore compatible with the methods of the disclosure. The RT can be a natural or engineered RT.” The reverse transcriptase will therefore be interpreted as encompassing any reverse transcriptase.
Claim 1 recites the limitation “placing the bacterial cell in conditions that allow the reverse transcription of the gene L, thereby generating altered copies of said gene L of the tpRNA.” The limitation “thereby generating altered copies of said gene L of the tpRNA” is interpreted as functional language as it does not require additional structural limitations and does not require additional method steps. The limitation will therefore be interpreted as the bacterial cell being in any conditions that allow for reverse transcription to occur.
The arrangement of the molecular complex is interpreted is accordance with the structure shown in Fig. 4(D), reproduced below:
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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.
Claim 1 is 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.
Regarding claim 1, it is unclear how the reverse transcription of the gene L generates altered copies of said gene L of the tpRNA. It is unclear whether reverse transcription, using any reverse transcriptase, will necessarily produce altered copies of gene L, or whether a specific reverse transcriptase or type of reverse transcriptase is required, or whether there is a specific method step which results in the altered copies of the gene L. Under the broadest reasonable interpretation, the claim encompasses any reverse transcriptase. However, pg. 25, lines 28-32 and pg. 26, lines 1-2, of the specification states that the reverse transcriptase (RT) is a low-fidelity RT and/or an RT with a high initiation rate/processivity. It is unclear from the claim how any reverse transcriptase results in altered copies of the gene L.
Allowable Subject Matter
Claim 1 is free of the prior art. The prior art does not teach or suggest the method for generating diversity in a gene by providing a bacterial cell comprising the molecular complex formed by the association of:
a scaffold protein (SP),
a template RNA (tpRNA) comprising from 5' to 3': the gene L, an RTtag sequence operably linked to the gene L and a scaffold protein binding module 1 (SPBM1) sequence capable of binding to the SP at a first specific binding site (SPS 1),
a primer RNA (prRNA) comprising: an RTprimer sequence positioned in 3' end of the prRNA and capable of complementary pairing to the RTtag sequence, a scaffold protein binding module 2 (SPBM2) sequence capable of binding to the SP at a second specific binding site (SPS2) and a reverse transcriptase binding module (RBM) sequence,
a fusion protein (RBD-RT) comprising a reverse transcriptase (RT) and an RBM binding domain (RBD) capable of binding to the RBM of the prRNA;
and placing the bacterial cell in conditions that allow the reverse transcription of the gene L, thereby generating altered copies of said gene L of the tpRNA.
Farzadfard et al. (Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science. 346(6211), 2014, 1256272) teaches a retron cassette which encodes three components in a single transcript: an RT protein, an RT primer, and the template for the reverse transcriptase (pg. 1256272-1, col. 3, par. 2; Fig. 1A, 1C, 1D).
However, the claims require the use of two scaffold protein binding module sequences and a scaffold protein. Farzadfard does not teach or suggest that the template RNA and the primer RNA are bound to a scaffold protein in the manner required by the claims.
WO 2021/081367 A1 is relevant to the claim, but does not teach or suggest the molecular complex as required by the claim.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Randi L Beil whose telephone number is (571)272-1147. The examiner can normally be reached M-F 8:00 am - 5:00 pm.
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/R.L.B./Examiner, Art Unit 1684
/AARON A PRIEST/Primary Examiner, Art Unit 1681