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 .
FINAL DETAILED ACTION
1. Applicant’s response filed on February 18, 2026 is acknowledged. Claims 1, 3-10, 12, 15, 17-21, 24-27 and 30 are currently pending. Claim 1 has been amended. Claim 30 was previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 1, 3-10, 12, 15, 17-21, and 24-27 are currently under examination.
Information Disclosure Statement
2. The information disclosure statement (IDS) submitted on February 18, 2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner. An initialed copy is attached hereto.
Objections Withdrawn
3. In view of Applicant’s amendment, the objection to claim 1 for informalities is withdrawn.
Rejections Withdrawn
4. In view of Applicant’s amendment, the rejection of claim(s) 1, 3-10, 12, 15, 17, 20, 21, and 24-27 under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by Pregibon et al., US 2016/0060682 A1; Published: 03/03/16 is withdrawn.
Objections Maintained
Claim Objections
5. The objection to claim 19 and as a result of the amendment claim 20 for depending upon a rejected based claim is maintained. Appropriate correction is required.
Rejections Maintained
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
6. The rejection of claims 1, 5-10, 12, 15, 18, 21 and 24-25 on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-10, 13, 15-16, and 19-20 of U.S. Patent No. 11,795,500 B2 is maintained for the reasons set forth in the previous Office action.
Although the claims at issue are not identical, they are not patentably distinct from each other because the pending claims are drawn to a method of identifying an RNA modification targets from a gene, the method comprising: contacting an RNA sample containing at least one modified nucleic acid with one or more oligonucleotide conjugated entities; ligating any RNA targets in the RNA sample to the one or more oligonucleotide conjugated entities by proximity-based ligation to form one or more chimeric RNA molecules; and identifying any RNA modification targets in the RNA sample based on the one or more chimeric RNA molecules.
Meanwhile, the combination of patented claims 1 and 20 anticipate and/or make obvious the pending claims.
1. A method of identifying RNA targets of RNA binding proteins, the method comprises:
contacting an RNA sample with one or more RNA binding proteins and an entity configured to bind the RNA binding protein to form a RNA-protein complex, the entity comprising one or more conjugated proximity oligonucleotides; and
ligating any RNA targets in the RNA sample to the one or more proximity oligonucleotides with proximity-based ligation to form one or more chimeric RNA molecules.
20. The method of claim 1, further comprising identifying a computationally chimeric RNA molecule of interest.
Applicant’s request to hold this rejection in abeyance is granted. The request for a terminal disclaimer remains in place until the claims are either amended or the claims are allowed and an approved terminal disclaimer has been filed. Until that time, the rejection is maintained.
New Grounds of Rejection Necessitated by Amendment
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
7. Claims 1, 3-10, 12, 15, 17, 18 and 24-27 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-9, 12, 15, 17, 18, 24-27 of copending Application No. 18/148,039 (reference application US20230250417). Although the claims at issue are not identical, they are not patentably distinct from each other because the pending claims are drawn to a method of identifying RNA modification targets from a gene, the method comprising: contacting an RNA sample containing at least one modified nucleic acid with one or more oligonucleotide conjugated entities comprising an antibody conjugated to an oligonucleotide barcode, the antibody targeting RNA modification targes; ligating any RNA targets in the RNA sample to the one or more oligonucleotide conjugated entities by proximity-based ligation to form one or more chimeric RNA molecules by ligating the RNA sample to the oligonucleotide barcode conjugated to the antibody; and identifying any RNA modification targets in the RNA sample based on the one or more chimeric RNA molecules.
Meanwhile the combination of co-pending claims anticipate or makes obvious the co-pending invention.
1. A method of identifying RNAs associated with translational machinery, the method comprising: contacting an RNA sample containing at least one component of a translational machinery with one or more oligonucleotide conjugated entities;
ligating any RNA targets in the RNA sample to the one or more oligonucleotide conjugated entities by proximity-based ligation to form one or more chimeric RNA molecules; and
identifying any RNA in the RNA sample associated with the translational machinery based on the one or more ligated chimeric RNA molecules.
27. The method of claim 1, wherein the one or more oligonucleotide conjugated entities comprises an oligo-barcoded sequence.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
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.
(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.
8. Claim(s) 1, 3, 4-7, 12, 15, 17, 18 and 24-27 are rejected under 35 U.S.C. 102(a)(1)/102(a)(2) as being anticipated by Lewis et al., US 2015/0011398; Published: 1/8/15.
Independent claim 1 is drawn to a method of identifying RNA modification targets from a gene, the method comprising: contacting an RNA sample containing at least one modified nucleic acid with one or more oligonucleotide conjugated entities comprising an antibody conjugated to an oligonucleotide barcode, the antibody targeting RNA modification targes; ligating any RNA targets in the RNA sample to the one or more oligonucleotide conjugated entities by proximity-based ligation to form one or more chimeric RNA molecules by ligating the RNA sample to the oligonucleotide barcode conjugated to the antibody; and identifying any RNA modification targets in the RNA sample based on the one or more chimeric RNA molecules.
Lewis teaches a method for identifying RNAs bound by RNA binding proteins comprising:
contacting an RNA sample with one or more oligonucleotide conjugated entities; ligating any RNA targets in the RNA sample to the one or more oligonucleotide conjugated entities by proximity-based ligation to form one or more chimeric RNA molecules; and identifying any RNA in the RNA sample associated with the RNA binding protein based on the one or more ligated chimeric RNA molecules (see Example 3 and paragraph 0055). Lewis teaches that the oligonucleotide conjugated entities comprise barcode sequences capable of identifying the one or more chimeric RNA molecules (see paragraphs 0054-55). Lewis teaches that the method can be carried out with as few as two or as many as 50,000 different proteins (see paragraph 0037), and that the antibodies each have a unique oligo (see paragraph 0054-55). Lewis teaches isolating the ligated RNA (see paragraph 0055).
Lewis teaches identifying a computationally chimeric RNA molecule of interest .The instant specification does not define what it means for a chimeric RNA to be “computationally” chimeric, and this is not a term of art. As Lewis teaches identifying the sequence of the chimeric oligonucleotides and using this to identify the RNA binding protein via the signature oligo, which identifies the antibody, which identifies the protein and the RNA sequence where it binds (see paragraph 0055). This chimeric molecule taught by Lewis is a “computationally” chimeric molecule since it is a chimera of the signature oligo and the sequence of the bound RNA.
Moreover, the sample is UV cross-linked (see paragraph 0055). Said method amplifies the chimeric RNA molecules to produce an amplified product (see paragraph 0052). Lewis teaches identifying the sequence of the chimeric oligonucleotides and using this to identify the RNA binding protein via the signature oligo, which identifies the antibody, which identifies the protein and the RNA sequence where it binds (see paragraph 0055). Lewis teaches wherein the one or more oligonucleotide conjugated entities comprises an oligo-barcoded sequence (see paragraph 0054-55).
Regarding claim 17, the claim only appears to require the recited RNA binding proteins are present, there is no action required such as binding the RNA binding proteins. As these are ubiquitously expressed binding proteins, it would have been inherent that they were present in the HEK293 cells taught by Lewis.
Conclusion
9. No Claim is allowed.
10. 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.
11. Any inquiry concerning this communication or earlier communications from the examiner should be directed to LAKIA J JACKSON-TONGUE whose telephone number is (571)272-2921. The examiner can normally be reached Monday-Friday 930AM-530PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571) 272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LAKIA J JACKSON-TONGUE/Examiner, Art Unit 1645 June 13, 2026
/BRIAN GANGLE/Primary Examiner, Art Unit 1645
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