DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
2. Applicant’s election of Group I in the reply filed on 3 June 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 23 and 25-27 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 3 June 2026.
Claims 1-3, 5-6, 8, 10-13, 15-16, and 18-21 are under prosecution.
Specification
3. The substitute specification filed 3 June 2026 is entered.
Drawings
4. The drawings were received on 19 September 2024 and the replacement sheet was received on 3 June 2026. These drawings are accepted.
Specification
5. The use of trade names or marks used in commerce (including but not necessarily limited to Tween), has been noted in this application. Any trade names or marks should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear 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.
Information Disclosure Statement
6. The Information Disclosure Statements filed 4 December 2024 and 3 June 2026 are acknowledged and have been considered.
It is noted that 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.
Claim Objections
7. Claim 19 is objected to because of the following informalities: claim 19 contains the text “and a (ii) a polynucleotide,” which appears to be a typographical error. Appropriate correction is required.
Claim Rejections - 35 USC § 112
8. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
9. Claim 16 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
This is a new matter rejection.
Claim 16 recites modified molecular brakes that “bind the polynucleotide but do not function as a polynucleotide binding protein.” What the parent Applications (now U.S. Patent Nos. 10,480,026 and 11,021,747) discuss helicases modified in the claimed manner, the parent Applications do not provide support for the broadly claimed modified “molecular brakes,” which encompass molecules other than the helicases discussed therein. Thus, because the claim encompasses embodiments not contemplated by the parent Applications, the claim includes new matter.
10. 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.
11. Claims 5-6, 8, 12-13, 16, and 19-21 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.
A. Claim 5 is indefinite in the recitation “is attached.” It is unclear if the attachment is an active method step required by the instant claim.
B Claim 6 is indefinite in the recitation “is ligated.” It is unclear if the attachment is an active method step required by the instant claim.
C. Claim 12 is indefinite in the recitation “the membrane,” which lacks antecedent basis because there is no previous recitation of a “membrane.”
D. Claim 13 is indefinite in the recitation “the polynucleotide binding domain,” which lacks antecedent basis because there is no previous recitation of a “polynucleotide binding domain.
E. Claim 16 is indefinite in the recitation “the polynucleotide,” which lacks antecedent basis in the previous recitations of an “RNA polynucleotide” and a “single stranded DNA polynucleotide.”
F. Claim 19 (upon which claims 20-21 depend) is indefinite in the recitation “modified to comprise a non-RNA polynucleotide and a (ii) a polynucleotide binding protein.” It is unclear if the phrase “and a (ii)” means the RNA polynucleotide is also modified with a polynucleotide binding protein.
Claim Interpretation
12. Claim 16 recites molecular brakes “that are modified such that they bind the polynucleotide but do functions as a polynucleotide binding protein.” Thus, because the molecular brake is required to bind the polynucleotide, the molecular brake as claimed cannot be a protein (i.e., the modified brake cannot simultaneously be a protein that binds a polynucleotide and yet not be a polynucleotide binding protein).
Claim Rejections - 35 USC § 103
13. 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.
14. 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.
15. Claims 1-3, 5-6, 8, 10-12, and 18-21 are rejected under 35 U.S.C. 103 as being unpatentable over Clarke et al. (PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006).
Regarding claim 1, Clarke et al. teach a method of characterizing, via sequencing, a target RNA molecule (page 1), comprising providing an RNA polynucleotide which is modified with a non-RNA polynucleotide, in the form of a DNA polynucleotide, thus forming an RNA/DNA chimera hybrid (e.g., Example 13 and Figure 14). Clarke et al. also teaching contacting the nucleic acid molecules (e.g., DNA) with a helicase, which controls the movement of a polynucleotide through the nanopore (page 6). The nanopore is a transmembrane pore (page 1), and measurements indicative of one or more characteristics of the polynucleotide, in the form of current measurements which estimate the sequence, are taken, thereby characterizing the target sequence of the polynucleotide (page 42). Clarke et al. also teach the method has the added advantage of allowing discrimination of each nucleotide with high sensitivity (page 31). Thus, Clarke et al. tach the known techniques discussed above.
Clarke et al. do not explicitly teach the helicase is a functionally equivalent DNA helicase that acts on a molecule that includes RNA.
However, Shin et al. teach a method wherein DNA helicases are used on double stranded molecules that include RNA and DNA (e.g., DNA-RNA hybrids; Abstract), and that the helicase have the added advantage of moving along the hybrid duplex without major difficulty (page 26921, first paragraph). Thus, Shin et al. teach the known techniques discussed above.
With respect to the order of mixing the polynucleotides, helicase, and transmembrane pore, the courts have held that selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Burhans, 154 F.2d 690, 69 USPQ 330 (CCPA 1946). See MPEP 2144.04 IV.C.
It is noted that the subject matter of a properly construed claim is defined by the terms that limit its scope. It is this subject matter that must be examined. As a general matter, the grammar and intended meaning of terms used in a claim will dictate whether the language limits the claim scope. Language that suggests or makes optional but does not require steps to be performed or does not limit a claim to a particular structure does not limit the scope of a claim or claim limitation. “Thereby” clauses are examples of language that may raise a question as to the limiting effect of the language in a claim. See MPEP 2106 [R-5] II c and MPEP § 2111.04.
It is also noted that a “wherein” clause, which is analogous to the “thereby” clause at the end of the instant claim, must give “meaning and purpose to the manipulative steps.” See, e.g., Griffin v. Bertina, 283 F.3d 1029, 1034, 62 USPQ2d 1431 (Fed. Cir. 2002).
MPEP 716.01(c) makes clear that “[t]he arguments of counsel cannot take the place of evidence in the record” (In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965)). Thus, counsel’s mere arguments cannot take the place of evidence in the record.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Clarke et al. with the teachings of Shin et al. to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the modification because said modification would have resulted in a method having the allowing discrimination of each nucleotide with high sensitivity as explicitly taught by Clarke et al. (page 31) as well as the added advantage of moving along the hybrid duplex without major difficulty as explicitly taught by Shin et al. (page 26921, first paragraph) using the functionally equivalent helicase of Shin et al.. In addition, it would have been obvious to the ordinary artisan that the known techniques of Shin et al. and Clarke et al. could have been combined with predictable results because the known techniques of Shin et al. and Clarke et al. predictably result in helicases and doubles stranded molecules suitable for sequencing applications.
Regarding claims 2-3, the method of claim 1 is discussed above. Clarke et al. teach a DNA adaptor, in the form of a leader sequence, is part of the non-RNA polynucleotide (Figure 14).
In addition, Shin et al. teach sequences (i.e., substrates: for helicases (page 26916, last paragraph of column 1). Thus, because it is the RNA that is being sequenced, it would have been obvious for the non-RNA sequence to comprise a DNA helicase binding site.
Applicant is again cautioned to avoid merely relying upon counsel's arguments in place of evidence in the record.
Regarding claims 5-6, the method of claim 1 is discussed above. Clarke et al. teach the non-RNA polynucleotide and the RNA polynucleotide are covalently linked by reactive groups on each of the polynucleotides; namely, they two are ligated together (i.e., claim 6; Example 13). Ligation requires a reaction between a reactive phosphate group on one strand and a reactive hydroxy group on the other strand (i.e., claim 5).
Regarding claim 8 the method of claim 1 is discussed above. Clarke et al. teach the characteristic measured is the sequence of the RNA polynucleotide (page 42).
Regarding claim 10, the method of claim 1 is discussed above. Clark et al. teach the measurements indicative of one or more characteristics of the polynucleotide are in the form of current measurements, which estimate the sequence, thereby characterizing the target sequence of the polynucleotide (page 42).
In addition, with respect to claim 10, it is reiterated that “thereby” clauses are examples of language that may raise a question as to the limiting effect of the language in a claim, and that a “wherein” clause, which is analogous to the “thereby” clause at the end of the instant claim, must give “meaning and purpose to the manipulative steps.”
Regarding claim 11, the method of claim 1 is discussed above. Clarke et al teach the RNA polynucleotide is modified with a cholesterol tag (Figure 14). It is noted that the claim does not state how the tag is used.
Regarding claim 12, the method of claim 1 of claim 1 is discussed above. Clarke et al. teach the RNA polynucleotide comprises a cholesterol anchor (i.e., tag; Figure 14), and that the tags are used to enrich nucleic acids (e.g., DNA) to a bilayer in the nanopore (Example 9). Thus, it would have been obvious to use the cholesterol tag on the RNA polynucleotide to anchor it to the membrane.
Regarding claim 18, the method of claim 1 is discussed above. Clarke et al. teach pores derived from MspA (pages 1-2).
Regarding claim 19, Clarke et al. teach a method of moving a target RNA molecule through a nanopore (page 1), comprising providing an RNA polynucleotide which is modified with a non-RNA polynucleotide, in the form of a DNA polynucleotide, thus forming an RNA/DNA chimera hybrid (e.g., Example 13 and Figure 14). Clarke et al. also teaching contacting the nucleic acid molecules (e.g., DNA) with a helicase, which controls the movement of a polynucleotide through the nanopore (page 6), wherein the nanopore is a transmembrane pore (page 1). Clarke et al. also teach the method has the added advantage of allowing discrimination of each nucleotide with high sensitivity (page 31). Thus, Clarke et al. tach the known techniques discussed above.
Clarke et al. do not explicitly teach the helicase is a functionally equivalent DNA helicase that acts on a molecule that includes RNA.
However, Shin et al. teach a method wherein DNA helicases are used on double stranded molecules that include RNA and DNA (e.g., DNA-RNA hybrids; Abstract), and that the helicase have the added advantage of moving along the hybrid duplex without major difficulty (page 26921, first paragraph). Thus, Shin et al. teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Clarke et al. with the teachings of Shin et al. to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the modification because said modification would have resulted in a method having the allowing discrimination of each nucleotide with high sensitivity as explicitly taught by Clarke et al. (page 31) as well as the added advantage of moving along the hybrid duplex without major difficulty as explicitly taught by Shin et al. (page 26921, first paragraph) using the functionally equivalent helicase of Shin et al.. In addition, it would have been obvious to the ordinary artisan that the known techniques of Shin et al. and Clarke et al. could have been combined with predictable results because the known techniques of Shin et al. and Clarke et al. predictably result in helicases and double stranded molecules suitable for sequencing applications.
Regarding claim 20, the method of claim 19 is discussed above.
With respect to the order of mixing the polynucleotides, helicase, and transmembrane pore, it is reiterated that the courts have held that selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results.
Applicant is again cautioned to avoid merely relying upon counsel's arguments in place of evidence in the record.
Regarding claim 21, the method of claim 19 is discussed above. Clarke et al. teach a DNA adaptor, in the form of a leader sequence, is part of the non-RNA polynucleotide (Figure 14).
In addition, Shin et al. teach sequences (i.e., substrates: for helicases (page 26916, last paragraph of column 1). Thus, because it is the RNA that is being sequenced, it would have been obvious for the non-RNA sequence to comprise a DNA helicase binding site.
Applicant is again cautioned to avoid merely relying upon counsel's arguments in place of evidence in the record.
16. Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Clarke et al. (PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006) as applied to claim 1 above, and further in view of DiPasquale et al. (U.S. Patent Application Publication No. US 20140234834 A1, published 21 August 2014) or Kong et al. (U.S. Patent Application Publication No. US 2004/0058378 A1, published 25 March 2004).
Regarding claim 15, the method of claim 1 is discussed above in Section 15.
Neither Clarke et al. nor Shin et al. teach the claimed functionally equivalent helicases.
However, Di Pasquale et al. teach the use of Dda helicases with RNA-DNA hybrids, which has the added advantage of allowing isothermal amplification of nucleic acids (paragraphs 0036-0037). In addition Kong et al. teach a method wherein RNA DNA hybrids (paragraph 0056) are used with helicases, including RecD, which has the added advantage of allowing exceptional processivity (paragraph 0087). Thus, Di Pasquale et al. and Kong et al. teach the use of the known functionally equivalent DNA helicases with RNA-DNA hybrids.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method taught by Clarke et al. and Shin et al. with the functionally equivalent helicases of either Di Pasquale et al. or Kong et al. to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the modification because said modification would have resulted in a method having the added advantage of either allowing isothermal amplification as explicitly taught by Di Pasquale et al. (paragraphs 0036-0037) or, alternatively, the added advantage of allowing exceptional processivity as explicitly taught by Kong et al. (paragraph 0087). In addition, it would have been obvious to the ordinary artisan that the known techniques of either Di Pasquale et al. or Kong et al. could have been applied to the method of Clarke et al. and Shin et al. with predictable results because the known techniques of either Di Pasquale et al. or Kong et al. predictably result in helicases suitable for use with RNA-DNA hybrids.
17. Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Clarke et al. (PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006) as applied to claim 1 above, and further in combination with Barrall et al. (PCT International Patent Application Publication No. WO2012/178093 A1, published 27 December 2012).
Regarding claim 16, the method of claim 1 is discussed above.
Neither Clarke et al. nor Shin et al. teach the claimed brake.
However, Barrall et al. teach methods of nanopore sequencing utilizing molecular brakes, in the form of modified hemolysin proteins altered to have larger amino acids to constrict the nanopore rather than alter binding of the nucleic acids, which have the added advantage of increasing the signal to noise ratio (page 28, “Modifications” and Abstract). Thus, Barrall et al. teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Barrall et al. with the cited prior art to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a method having the added advantage of increasing the signal to noise ratio as explicitly taught by Barrall et al. (page 28, “Modifications” and Abstract). In addition, it would have been obvious to the ordinary artisan that the known techniques of Barrall et al. could have been applied to the cited prior art with predictable results because the known techniques of Barrall et al. predictably result in useful nanopores for nucleic acid detection.
18. Claims 1-3, 5-6, 8, 10-12, and 18-21 are rejected under 35 U.S.C. 103 as being unpatentable over Clarke et al. (U.S. Patent Application Publication No. US 2014/0186823 A1, published 3 July 2014) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006) based on the citations presented above.
US 2014/0186823 A1 is the National Stage Entry of PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012, and thus contains the same subject matter.
19. Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Clarke et al. (U.S. Patent Application Publication No. US 2014/0186823 A1, published 3 July 2014) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006) as applied to claim 1 above, and further in view of DiPasquale et al. (U.S. Patent Application Publication No. US 20140234834 A1, published 21 August 2014) or Kong et al. (U.S. Patent Application Publication No. US 2004/0058378 A1, published 25 March 2004) based on the citations presented above.
As noted above, US 2014/0186823 A1 is the National Stage Entry of PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012, and thus contains the same subject matter.
20. Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Clarke et al. (U.S. Patent Application Publication No. US 2014/0186823 A1, published 3 July 2014) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006) as applied to claim 1 above, and further in combination with Barrall et al. (PCT International Patent Application Publication No. WO2012/178093 A1, published 27 December 2012).
As noted above, US 2014/0186823 A1 is the National Stage Entry of PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012, and thus contains the same subject matter.
Double Patenting
21. 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.
22. A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
23. A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
24. Claim 13 is rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 1 of prior U.S. Patent No. 10,480,026.
This is a statutory double patenting rejection.
25. 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.
26. Claims 1-3, 5-6, 8, 10-13, 15-16, and 18-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 10,392,658 in view of Clarke et al. (PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006).
Both sets of claims are drawn to moving a polynucleotide through a nanopore
using a helicase, molecular brakes, modified helicases that reduce the opening, and
double stranded polynucleotides. In addition both sets of claims are drawn to the same
types of helicases. Any additional limitations of the '658 claims are encompassed by the open claim language "comprising" found in the instant claims.
The ‘658 claims do not teach the non-RNA polynucleotide or characterizing.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Clarke et al. as discussed above.
Neither the ‘658 claims nor Clarke et al. teach a helicase that is a functionally equivalent DNA helicase that acts on a molecule that includes RNA.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Shin et al. as discussed above.
27. Claims 1-3, 5-6, 8, 10-13, 15-16, and 18-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 10,392,658 in view of Clarke et al. (U.S. Patent Application Publication No. US 2014/0186823 A1, published 3 July 2014) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006).
Both sets of claims are drawn to moving a polynucleotide through a nanopore
using a helicase, molecular brakes, modified helicases that reduce the opening, and
double stranded polynucleotides. In addition both sets of claims are drawn to the same
types of helicases. Any additional limitations of the '658 claims are encompassed by the open claim language "comprising" found in the instant claims.
The ‘658 claims do not teach the non-RNA polynucleotide or characterizing.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Clarke et al. as discussed above.
Neither the ‘658 claims nor Clarke et al. teach a helicase that is a functionally equivalent DNA helicase that acts on a molecule that includes RNA.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Shin et al. as discussed above.
28. Claims 1-3, 5-6, 8, 10-12, 15-16, and 18-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 10,480,026 in view of Clarke et al. (PCT International Application Publication No. WO 2012/107778 A2, published 16 August 2012) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006).
Both sets of claims are drawn to moving a polynucleotide through a nanopore
using a helicase, molecular brakes, modified helicases that reduce the opening, and
double stranded polynucleotides. In addition both sets of claims are drawn to the same
types of helicases. Any additional limitations of the '026 claims are encompassed by the open claim language "comprising" found in the instant claims.
The ‘026 claims do not teach the non-RNA polynucleotide or characterizing.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Clarke et al. as discussed above.
Neither the ‘026 claims nor Clarke et al. teach a helicase that is a functionally equivalent DNA helicase that acts on a molecule that includes RNA.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Shin et al. as discussed above.
29. Claims 1-3, 5-6, 8, 10-12, 15-16, and 18-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 10,480,026 in view of Clarke et al. (U.S. Patent Application Publication No. US 2014/0186823 A1, published 3 July 2014) and Shin et al. (J. Biol. Chem., vol. 281, pages 16914-16921, published online 7 July 2006).
Both sets of claims are drawn to moving a polynucleotide through a nanopore
using a helicase, molecular brakes, modified helicases that reduce the opening, and
double stranded polynucleotides. In addition both sets of claims are drawn to the same
types of helicases. Any additional limitations of the '026 claims are encompassed by the open claim language "comprising" found in the instant claims.
The ‘026 claims do not teach the non-RNA polynucleotide or characterizing.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Clarke et al. as discussed above.
Neither the ‘026 claims nor Clarke et al. teach a helicase that is a functionally equivalent DNA helicase that acts on a molecule that includes RNA.
However, this limitation, the remaining limitations, and the rationale for combining are taught by Shin et al. as discussed above.
30. Claims 1-3, 5-6, 8, 10-12, 15-16, and 18-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 11,021,747. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to methods of characterizing target RNA polynucleotides comprising non-DNA, adaptors, leaders, covalent attachment via reactive groups (e.g., ligation), solid state pores, polynucleotide binding proteins and/or molecular brakes (e.g., helicases), etc. Any additional limitations of the ‘747 claims are encompassed by the open claim language “comprising” found in the instant claims.
31. Claims 1-3, 5-6, 8, 10-13, 15, and 18-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12,129,518. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to methods of characterizing target RNA polynucleotides comprising non-DNA, adaptors, leaders, covalent attachment via reactive groups (e.g., ligation), solid state pores, polynucleotide binding proteins and/or molecular brakes (e.g., helicases), etc. Any additional limitations of the ‘516 claims are encompassed by the open claim language “comprising” found in the instant claims.
32. Claim 16 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12,129,518 as applied to claim 1 above, and further in combination with Barrall et al. (PCT International Patent Application Publication No. WO2012/178093 A1, published 27 December 2012) based on the citations and rationale provided above.
Prior Art
33. Guo (PCT International Patent Application Publication No. WO2010/062697 A2, published 3 June 2010: see also U.S. Patent Application Publication No. US 2015/0267253 A1, published 24 September 2015, which is the National Stage Entry of the PCT) is hereby made of record but is not relied upon for any rejection.
Guo teaches using nanopore methods utilizing molecular brakes (i.e., membrane-incorporated connector proteins) that partially obstruct or occlude the nanopore (page 35 of the PCT, paragraph 0080 of the National Stage), but does not teach the claimed RNA containing single stranded DNA or non-RNA polynucleotides.
Conclusion
34. No claim is allowed.
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Robert T. Crow
Primary Examiner
Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683
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