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 .
The preliminary amendment, filed November 2, 2025, cancelling claims 1-44 and adding new claims 45-63 is acknowledged and has been entered.
Claims 45-63 are pending.
Election/Restrictions
Applicant's election with traverse of Group III, claims 47 and 60 in the reply filed on August 10, 2026 is acknowledged. The traversal is on the ground(s) that “"the pending claims are directed to a single general inventive concept, namely the determination of molecular information from nucleic acids through hybridization of oligonucleotide probes. The various claim groups do not define different inventions, but rather different embodiments and outputs of the same underlying analytical platform" (p 1 of remarks). This is not found persuasive because there is not a single inventive concept because the main unifying feature between the claims is hybridization. The methods of Group I, II and III may share certain features, but the steps of the methods and the manner in which they are carried out are distinct and do not share a single inventive concept.
The requirement is still deemed proper and is therefore made FINAL.
Claims 45-46, 48-59 and 61-63 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 timely traversed the restriction (election) requirement in the reply filed on August 10, 2026.
Claims 47 and 60 are pending and will be examined.
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.
Claim(s) 47 and 60 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Taskova et al. (Org Biomol Chem, 2017, 15, 5680-5684).
With regard to claim 47, Taskova teaches a method of determining a sequence and epi-sequence of at least a portion of a nucleic acid molecule, comprising:
(i) fixing the nucleic acid molecule on a test substrate when the nucleic acid molecule is a single stranded molecule or denaturing the nucleic acid molecule to a single stranded molecule and fixing the single stranded nucleic acid molecule on the test substrate when the nucleic acid molecule is a double stranded molecule or fixing the nucleic acid molecule on the test substrate and denaturing the nucleic acid molecule on the test substrate to a single stranded molecule when the nucleic acid molecule is a double stranded molecule, thereby forming a fixed single stranded nucleic acid on the test substrate (Table 2, p. 5683; see also Abstract and p. 5684, col. 1);
(ii) exposing the fixed single stranded nucleic acid to a respective oligonucleotide probe species in a set of oligonucleotide probe species, wherein each respective oligonucleotide probe species of the set of oligonucleotide probe species is capable of hybridizing to its complementary portion located at one or more locations on the fixed single stranded nucleic acid and has:
- a unique respective predetermined sequence,
- a predetermined length, and
- a respective label selected from the group consisting of a dye, a fluorescent nanoparticle, a plasmon resonant particle, a light-scattering particle, a nanoparticle, and a fluorescence resonance energy transfer (FRET) partner which is capable of producing a fluorescent signal;
wherein the exposing step occurs under conditions such that:
- oligonucleotide probes of the respective oligonucleotide probe species of the set of oligonucleotide probe species repetitively transiently and reversibly bind to the one or more locations on the fixed single stranded nucleic acid on the test substrate,
thereby forming a respective transient heteroduplex on each of the one or more locations on the fixed single stranded nucleic acid on the test substrate, and
- respective instances of optical activity from the respective label are generated and detected by repetitively transiently and reversibly binding the oligonucleotide probes of the respective oligonucleotide probe species of the set of oligonucleotide probe species to the one or more locations on the fixed single stranded nucleic acid on the test substrate (Table 2, p. 5683; see also Abstract and p. 5684, col. 1);
(iii) determining if one or more portions of the fixed single stranded nucleic acid are complementary to the respective oligonucleotide probe species of the set of oligonucleotide probe species by measuring the respective instances of optical activity on each of the one or more locations on the fixed single stranded nucleic acid on the test substrate occurring during the exposing step using a two-dimensional imager capable of detecting the respective instances of optical activity generated from the respective label, thereby obtaining a first set of one or more positions on the fixed single stranded nucleic acid that are complementary to the respective oligonucleotide probe species of the set of oligonucleotide probe species (Table 2, p. 5683; see also Abstract and p. 5684, col. 1);
(iv) washing the test substrate to remove the respective oligonucleotide probe species of the set of oligonucleotide probe species from the test substrate;
(v) repeating steps (b)-(d) by exposing the fixed single stranded nucleic acid on the test substrate to another respective oligonucleotide probe species in the set of oligonucleotide probe species, thereby obtaining a second set of one or more positions on the fixed single stranded nucleic acid that are complementary to another respective oligonucleotide probe species in the set of oligonucleotide probe species (Table 2, p. 5683; see also Abstract and p. 5684, col. 1);
(vi) determining the sequence of at least the portion of the nucleic acid based at least in part on the first set of one or more positions on the fixed single stranded nucleic acid that are complementary to the respective oligonucleotide probe species of the set of oligonucleotide probe species and the second set of one or more positions on the fixed single stranded nucleic acid that are complementary to the another respective oligonucleotide probe species of the set of oligonucleotide probe species (Table 2, p. 5683; see also Abstract and p. 5684, col. 1); and
(vii) determining whether the portion of the nucleic acid molecule has an epigenetic modification based on an observed differential binding behavior of the oligonucleotide probes of the respective oligonucleotide probe species in the set of oligonucleotide probe species to their complementary portion located at one or more locations on the fixed single stranded nucleic acid when the one or more locations has an epigenetic modification compared to when the one or more locations does not have an epigenetic modification (p. 5683-5684, especially, p 5684 col. 1, where fluorescent LNA/DNA probes are tested for detection of epigenetic modifications).
With regard to claim 60, Taskova teaches a method of claim 47, wherein the binding profiles of each oligonucleotide capable of binding to a nucleic acid sequence that may bear a modification are characterized by testing against synthetic modified and non-modified versions of nucleic acid sequences that may bear a modification and thus serve as a reference to compare the binding profiles obtained for the sample molecules (p. 5683-5684, especially, p 5684 col. 1, where fluorescent LNA/DNA probes are tested for detection of epigenetic modifications).
Citation of Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Maki et al. (Biosensors and Bioelectronics, 2008, 23:780-787).
Conclusion
No claims are allowed. All claims stand rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE KANE MUMMERT whose telephone number is (571)272-8503. The examiner can normally be reached M-F 9:00-5:30.
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, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681
