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 .
Response to Amendment
The amendment filed 08/26/2025 is acknowledged. Regarding the Office action mailed 05/29/2025:
The objection to the specification is withdrawn in view of the substitute specification deleting hyperlinks.
The objection to claim 3 is withdrawn in view of the amendment.
Regarding the rejections of various claims under 35 USC 112(b), any rejection not reiterated below is withdrawn in view of the amendment. However, several rejections are maintained as they were not obviated by the amendment.
Regarding the rejection under 35 USC 102 over Chen, the rejection is maintained for two different reasons. The first reason has to do with the meaning of the “configured to” language of claim 1. This is explained in the new grounds of rejection under 35 USC 112(b) set forth below. The second reason has to do with some claims, such as claim 20, which only requires one of the components of claim 1.
Applicant’s arguments as to the rejections will be addressed following all rejections.
Claim Interpretation
Claim 1 has been amended to recite: “wherein the first programmable DNA nuclease polypeptide and the second programmable DNA nuclease polypeptide are each configured to bind, in a site-specific manner, to flanking sites of a donor target polynucleotide to excise a target polynucleotide”. The claim does not explicitly state the DNA nuclease polypeptides are the components that do the excising. The claim will be construed to mean that the site-specific binding of the programmable DNA nuclease polypeptides is necessary for the excision to occur, but the actual step of “excising” is not necessarily carried out by the programmable DNA nucleases. Support for this broader interpretation includes claim 9, which indicates the nucleases may lack nuclease activity, claims 14, 26 and 42, which refers to transposases as performing the excising, and Applicant’s remarks filed 08/26/2025: “…the present claims recite a four-component system in which first and second Class II transposase polypeptides are each fused to a distinct programmable nuclease and guided by separate guide RNAs to flank a first target polynucleotide…”. The specification (paragraph [0826]) reads: “In some embodiments, transposase mediated cleavage occurs by a transposase associated with or otherwise coupled or fused to the programmable DNA nuclease. In some embodiments, no nicking or nuclease activity occurs at the target site but rather a transposase associated with the programmable DNA nuclease cleaves at or near the target site of the programmable DNA nuclease.”
Therefore, the claims will be construed to broadly encompass the case where the programmable nucleases serve only to target the transposases, while the transposases catalyzes the excision.
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.
Maintained Rejections-35 USC 112(b)
Claim 2 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.
Claim 2 recites the limitation "the first target polynucleotide" in lines 2-3. There is insufficient antecedent basis for this limitation in the claim. Claim 2 depends from claim 1, which recites “a donor target polynucleotide”, but does not recite “a first target polynucleotide”.
Claim 14 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.
Claim 14 recites the limitation "the first target polynucleotide" in line 3 and lines 5-6. There is insufficient antecedent basis for this limitation in the claim. Claim 14 depends from claim 1, which recites “a donor target polynucleotide”, but does not recite “a first target polynucleotide”. Claim 14 also recites “the second target polynucleotide” in line 6. There is insufficient antecedent basis for this limitation in the claim. Claim 14 depends from claim 1, which recites “a recipient polynucleotide”, but does not recite “a second target polynucleotide”. Claim 14 recites “the Class II transposase polynucleotide” in lines 3-4. There is insufficient antecedent basis for this limitation in the claim. Claim 14 depends from claim 1, which does not recite a “Class II transposase polynucleotide”.
Claim 16 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.
Claim 16 recites the limitation "the first target polynucleotide" in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 16 depends from claim 1, which recites “a donor target polynucleotide”, but does not recite “a first target polynucleotide”.
Claims 26, 27, 29-31, 33-37, 39 and 40 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 26 recites the limitation "the first target polynucleotide" in step b and “the second target polynucleotide” in step d. There is insufficient antecedent basis for this limitation in the claim. While claim 1, from which claim 26 depends, refers to “a donor target polynucleotide” and “a recipient polynucleotide”, it does not recite a “first target polynucleotide” or a “second target polynucleotide”.
Claims 27, 29-31, 33-37, 39 and 40 depend directly or indirection from claim 26 and are rejected for the same reasons.
Claims 42, 43, 45-47, 49 and 50 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 42 recites the limitation "the first target polynucleotide" in step b and “the second target polynucleotide” in step d. There is insufficient antecedent basis for this limitation in the claim. While claim 1, from which claim 26 depends, refers to “a donor target polynucleotide” and “a recipient polynucleotide”, it does not recite a “first target polynucleotide” or a “second target polynucleotide”.
Claims 43, 45-47, 49 and 50 depend directly or indirection from claim 42 and are rejected for the same reasons.
New Rejections-35 USC 112(b)
Claim 20 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.
Claim 20 refers to “components (a)-(d) of claim 1”. Amended claim 1 does not designate any components as “a”, “b”, “c” or “d”. Appropriate correction is required.
Claims 1-9, 12-14, 16-17, 20-21, 23-27, 29-31, 33-37, 39-43, 45-47, 49-50 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 has been amended to recite “wherein the first programmable DNA nuclease polypeptide and the second programmable DNA nuclease polypeptide are each configured to bind, in a site-specific manner, to flanking sites of a donor target polynucleotide to excise a target polynucleotide”. Claim 1 also recites “wherein the first Class II transposase polypeptide and the second Class II transposase polypeptide are configured to insert the excised target polynucleotide into a recipient polynucleotide in a site-specific manner”.
The underlying disclosure of the specification explains how the invention works. The programmable nucleases bind DNA in a site-specific manner via complexation with a pair of guide RNA molecules (first and second “guide molecules”), which guide RNA molecules target the programmable nucleases to specific sites on a “first target polynucleotide”/“donor polynucleotide” complementary to such guide RNA molecules. The Class II transposases, which are complexed with the programmable nucleases, excise a segment of DNA from this “first target polynucleotide”/“donor polynucleotide”. Then, programmable nuclease/transposase complexes are targeted to a “second target polynucleotide”/“recipient polynucleotide” by a second pair of guide RNA molecules (third and fourth “guide molecules”), whereby the transposases insert the DNA segment into the “second target polynucleotide”/“recipient polynucleotide”. See figure 1. See also Applicant’s remarks in the reply filed 08/26/2025 (paragraph spanning pages 16-17 of the reply):
In contrast, the present claims recite a four-component system in which first and second Class II transposase polypeptides are each fused to a distinct programmable nuclease and guided by separate guide RNAs to flank a first target polynucleotide. After boundary-defined excision, the system inserts the excised polynucleotide into a second target polynucleotide using a second set of transposase-nuclease fusions, again guided by two additional guide RNAs. This structure enables both programmable excision and programmable integration, with defined boundaries at both donor and recipient sites-features entirely absent from Chen.
Therefore, both the excision and insertion are mediated by guide RNA molecules. However, claim 1 does not recite the guide RNA molecules. Claims 12 and 13, which ultimately depend from claim 1, do recite these “guide molecules” (claim 12 reciting the first and second guide molecules, claim 13 reciting the third and fourth guide molecules). The fact that these are not recited in claim 1, but are recited in claims 12 and 13, raises a question as to the meaning of “configured to bind” and “configured to insert” in claim 1.
One meaning of “configured to bind”/“configured to insert” is that claim 1 requires the first and second programmable nucleases to be complexed with the first and second guide molecules, such that the first and second programmable nuclease, as claimed, are in a state capable of site-specific binding to the “first target polynucleotide”/“donor polynucleotide”. This is problematic because that would mean that the first and second programmable nucleases would simultaneously have to be complexed with the third and fourth guide molecules, such that the first and second programmable nucleases are in a state capable of directing their associated Class II transposase polypeptides to the “second target polynucleotide”/“recipient polynucleotide”, such that the first and second Class II transposase polypeptides are “configured to insert” in a site-specific manner. The first and second programmable nucleases cannot be complexed to the first and second guide molecules, respectively, and simultaneously complexed to the third and fourth guide molecules, respectively. Note that claim 1 and figure 1 refer only to “first” and “second” programmable nucleases (which is understood to mean first and second molecules of programmable nuclease). Throughout the disclosure, the “first” guide molecule is described as forming a “first complex” with the “first programmable DNA nuclease”, the “second” guide molecule is described as forming a “second complex” with the “second programmable DNA nuclease”, the “third” guide molecule is described as forming a “third complex” with the “first programmable DNA nuclease”, and the “fourth” guide molecule is described as forming a “fourth complex” with the “second programmable DNA nuclease”. This suggests that, following the excision step, the first and second guide molecules dissociate from the first and second programmable DNA nucleases, and are replaced by the third and fourth guide molecules, respectively. Therefore, the first and second programmable DNA nuclease polypeptides cannot be “configured to bind” in a site-specific manner at the same time as the first and second Class II transposase polypeptides are “configured to insert” in a site-specific manner, since the first and third guide molecules cannot simultaneously complex with the first programmable DNA nuclease polypeptide, nor can the second and fourth guide molecules simultaneously complex with the second programmable DNA nuclease polypeptide.
The second meaning of “configured to bind”/“configured to insert” is that the programmable DNA nuclease polypeptides merely have to be capable of performing this function when provided with the requisite guide molecules. Under this interpretation, all that claim 1 requires is two molecules of a programmable nuclease-class II transposase complex. For this reason, certain of the previous prior art rejections are maintained and reiterated below.
Because of the two possible interpretations of claim 1, the first of which does not seem to be possible due to the fact that a programmable nuclease cannot simultaneously complex with two different guide RNAs, claim 1 is indefinite under 35 USC 112(b). As all claims ultimately depend from or reference claim 1, they are rejected for the same reason.
Claim Rejections - 35 USC § 102
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.
Claim(s) 1, 3-9, 12, 16, 17, 20, 21 and 23-25 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen (The CRISPR journal. 2019 Dec 1;2(6):376-94, previously cited).
Regarding claims 1 and 3, Chen disclosed the system as claimed. See Figure 1A:
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Note that the first programmable DNA nuclease polypeptide (dCas9) is shown binding site-specifically to a target polynucleotide, via a guide RNA (gRNA). The second programmable DNA nuclease polypeptide (also dCas9) is show complexed to its own guide RNA (which is presumable identical to the guide RNA of the first programmable DNA nuclease polypeptide), so it would be “capable” of site-specific binding to a target polynucleotide as well. Note that each programmable DNA nuclease polypeptide is coupled to its corresponding Class II transposase polypeptide via a “linker”. The transposase is Himar1 transposase, which is a Tc1/mariner transposase (page 376, second column), which is named in the instant specification (paragraph [0024] of substitute specification from 11/27/2023) as a Class II transposon polypeptide.
Regarding claims 4-7, as noted above, the programmable DNA nuclease polypeptide is dCas9 (i.e. Cas9, which is a Class 2 Type II Cas polypeptide).
Regarding claims 8 and 9, dCas9 means “dead” Cas9, which refers to the fact that it lacks nuclease activity; see abstract and page 377, second column, first paragraph; see also paragraph [0187] of the substitute specification from 11/27/2023.
Regarding claim 12, Chen disclosed an experiment in which Himar-dCas9, along with two different gRNAs targeting mCherry, were expressed in an E. coli strain with a genomically integrated mCherry gene; see page 385, second column, last paragraph and Table 2. Because gRNA_5 and gRNA_16 are different sequences, they are capable of directing Himar-dCas9 to bind different sequences of mCherry. [Note, while claim 1 as amended refers to “flanking sites of a donor”, claim 12 does not equate “a first target sequence of a first target polynucleotide” and “a second target sequence of the first target polynucleotide” to the “flanking sites of a donor”.]
Regarding claim 16, the target polynucleotide into which Chen’s system inserted the transposon donor did not contain any transposon long terminal repeats. Insertion of the transposon merely required a “TA” dinucleotide appropriately spaced relative to the guide RNA binding site; see Figure 1A.
Regarding claim 17, as noted above, Himar is a Tc1/mariner transposon.
Regarding claims 20, 21, 23 and 24, Chen disclosed a vector (and a cell/cell population containing such vector) encoding Himar-dCas9; see, e.g., page 379, last paragraph: “Himar-dCas9…expressed in MG1655 E. coli from tet-inducible expression vector[] pHdCas9…”. See also Table 1 details for pHdCas9: “Himar-dCas9 on tet-inducible promoter”. Note that an E. coli cell also qualifies as “an organism”.
Regarding claim 25, Chen disclosed a lipofection reagent for transfecting mammalian cells comprising Lipofectamine 2000 and pHdCase9-mammalian expression plasmid (page 385, first column, last paragraph). Lipofectamine 2000 falls within the broadest reasonable definition of a “pharmaceutically acceptable carrier”.
As to the “configured to bind” and “configured to insert” language of amended claim 1, under the interpretation that such language means the programmable DNA nuclease polypeptides and associated Class II transposase polypeptides merely have to be capable of performing these functions when provided with the requisite guide molecules, the Himar-dCas9 constructs are inherently capable of performing these actions when they are provided with the appropriate guide RNA molecules. See discussion in the rejection of claim 1 under 35 USC 112(b) above.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 41 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chen (The CRISPR journal. 2019 Dec 1;2(6):376-94, previously cited) in view of Hew (Synthetic Biology 2019, 4(1): ysz018, public availability date 2 July 2019; IDS reference).
The disclosure of Chen has been discussed. Chen did not disclose or suggest use of such system as a therapy or treatment, and so did not suggest administering the system to “a subject in need thereof”.
In the same field of endeavor, Hew disclosed a similar system, except that dCas9 was fused to the piggyBac transposase; see Figure 1. Hew specifically suggested such an approach for therapies. See abstract: “Safer and more efficient methods for directing therapeutic genes to specific sequences could increase the repertoire of treatable conditions…These vectors expand the utility of the piggyBac system for applications in targeted gene addition for biomedical research and gene therapy.” See also page 10, sentence spanning two columns: “A strictly site-specific, RNA-guided transposase would have important applications including transgenic animal generation, modification of cell lines for research and diagnostics or delivery of therapeutic cargo to a designated location in the genome.”
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to adapt Chen’s system to deliver a therapeutic target nucleic acid, and administer it to “a subject in need thereof”, since Hew suggested this use for gRNA-mediated transposition.
Response to Arguments
Applicant's arguments filed 08/26/2025 have been fully considered but they are not persuasive. Applicant argues distinction over Chen based on the functional language of amended claim 1. However, as explained in the new rejection under 35 USC 112(b), the functional language (“configured to”) lends itself to different interpretation owing to: (1) the lack of any detail as to how the elements are “configured to” perform the function (namely, the absence from claim 1 of any recitation of the guide molecules (guide RNAs) that actually allow this function to be carried out), and (2) the problem of having both the programmable DNA nucleases and the transposases being “configured” to perform a function when each function is dependent on a different guide molecule complexing with the nucleases, which nucleases can only complex with one guide molecule at a time. Based on these issues, a reasonable interpretation is that “configured to” means nothing more than that the nucleases are capable of being targeted to the different sites if and when appropriate guide molecules are supplied to them. Under this latter interpretation, the rejections under 35 USC 102 and 103 are still proper and therefore maintained.
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 SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
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/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
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