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 .
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.
Claims 1-9, 11-14 and 16-21 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.
On line 17 of claim 1, the phrase “or a magnetic characteristic” should be deleted since claim 1 has been amended to recite that the moiety attached to each nucleotide of the set of nucleotides is capable of causing a current signal in the tunneling junction, and the characteristic measured by the meter device is recited as being a characteristic through the first conductor and the second conductor via the moiety. Therefore, only an electrical characteristic representative of the current signal caused by the moiety would be measured by the meter device. On line 24 of claim 1, the phrases “the first electrode” and “the second electrode” lack antecedent basis since claim 1 does not positively recite the first and second conductors as being first and second electrodes.
Claim 7 is indefinite since it recites that the first electrode comprises gold, silver, platinum or palladium. However, claim 1 has been amended to recite that the first conductor and the second conductor (i.e. electrodes as recited in claim 4 from which claim 7 depends) comprise ferromagnetic materials, and none of gold, silver, platinum or palladium are ferromagnetic materials. Therefore, claim 7 should be canceled.
On line 1 of claim 17, the phrase “wherein the nucleotide” should be changed to –wherein each nucleotide--.
On line 14 of claim 21, the phrase “or a magnetic characteristic” should be deleted since claim 21 recites that the moiety attached to each nucleotide of the set of nucleotides is capable of causing a current signal in the tunneling junction, and the characteristic measured by the meter device is recited as being a characteristic through the first conductor and the second conductor via the moiety. Therefore, only an electrical characteristic representative of the current signal caused by the moiety would be measured by the meter device. On line 21 of claim 21, the phrases “the first electrode” and “the second electrode” lack antecedent basis since claim 21 does not positively recite the first and second conductors as being first and second electrodes.
Inventorship
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 Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claim(s) 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Oldham et al . (WO 2017/189930, submitted in the IDs filed on June 26, 2023) in view of Turner et al (US 2016/0083789, cited in the last Office action mailed on February 25, 2026).
With regards to claim 21, Oldham et al teach of a system for analyzing nucleic acid molecules (see paragraph 0005 in Oldham et al where it states “Some aspects of the present disclosure provide systems for sequencing polynucleotide molecules such as DNA”) comprising: a tunneling junction comprising a first conductor and a second conductor separated by an insulating layer (see paragraph 0005 in Oldham et al where it states “The systems may comprise two electrodes disposed on a substrate separated by a non-conductive gap”, wherein the two electrodes constitutes a first conductor and a second conductor, and paragraph 0189 in Oldham et al where it states “In some cases, a target complex may be bound to a dielectric which may comprise a material used to form a gap between electrodes of an electrode pair, which may be silicon nitride, silicon oxide… or other standard semiconductor dielectric materials”, wherein the dielectric material forming the non-conductive gap between the electrodes of the tunneling junction constitutes an insulating layer), a polymerase attached to the tunneling junction and connected to a template parent strand, the polymerase configured to elongate a nascent strand that is hybridized to the template parent strand (see paragraph 0006 in Oldham et al where it states “The electrodes and the gap may be configured to accommodate a polymerase in the vicinity of the two electrodes. The electrodes and the gap may be adapted for detecting an electron or hole tunneling current during incorporation and or binding of a nucleotide into a polynucleotide in the presence of the polymerase. The nucleotide may comprise a tunneling label. The nucleotide may be incorporated into or bound to a single stranded portion of the polynucleotide”, and paragraph 0200 in Oldham et al where it states “A polymerase may be provided with a primed target nucleic acid strand, wherein a single stranded portion may provide a template for incorporation (addition) of complementary nucleotides, which may be nucleotides with tunneling labels), a power supply in electrical communication with at least one of the first conductor and the second conductor (i.e. the first and second electrodes) (see Figures 2B-2D in Oldham et al which depict a power supply in electrical communication with the first electrode 202A of the tunneling junction on the left-hand side of the tunneling junction), a set of nucleotides, each nucleotide of the set of nucleotides attached to a label compound comprising a moiety (see paragraph 0006 in Oldham et al where it states “The electrodes and the gap may be adapted for detecting an electron or hole tunneling current during incorporation and or binding of a nucleotide into a polynucleotide in the presence of the polymerase. The nucleotide may comprise a tunneling label.”, paragraph 0201 in Oldham et al where it states “an enzyme or polymerase may be considered to be in a vicinity of a gap between two electrodes when a labeled moiety bound by an enzyme or polymerase may be able to bind or interact with both electrodes such that a measurable tunneling current may be detected as a result of an interaction of the label bound to a labeled moiety with both electrodes.”, and paragraph 0202 in Oldham et al where it states “Incorporation or binding of a base with a tunneling label may cause an increase in tunneling current going from one electrode to another.”), a meter device configured to measure a value of a characteristic through the first conductor and the second conductor via the moiety, wherein the characteristic is an electrical characteristic (see Figures 2B-2D in Oldham et al which depict a meter A in communication with the second electrode 202B of the tunneling junction on the right-hand side of the tunneling junction, and see paragraphs 0201-0202 in Oldham et al), and a non-transitory computer readable medium storing a plurality of instructions that when executed by a processor, cause the processor to perform the steps of the method to measure a value of the electrical characteristic through the first and second electrodes when the labeled moiety on a nucleotide of the set of nucleotides binds to a complementary nucleotide on the template parent polynucleotide strand attached to the polymerase on the tunneling junction, and measure a background value of the electrical characteristic of the tunneling junction when no labeled nucleotide from the set of nucleotides is bound to the polymerase and template parent strand as a baseline “no-current” reference value (see paragraph 0021 in Oldham et al where it states “Another aspect of the present disclosure provides a non-transitory computer-readable medium comprising machine-readable code that, upon execution by one or more computer processors, implements a method for sequencing a nucleic acid molecule…”, paragraph 0205 in Oldham et al where it states “During this time wherein no nucleotide and associated label 205 may be bound by a polymerase or other enzyme 206, essentially no current may flow between electrodes 202A and 202B.”, and paragraph 0330 where it states “A background signal may be determined from sensors which may not have bound enzymes, and may thus not have signals.”). See Figures 2B-2D, and paragraphs 0004-0015, 0020, 0024, 0189, 0200-0205, 0314 and 0330 in Oldham et al.
Oldham et al fail to teach that the instructions provided by the non-transitory computer readable medium cause the processor to compare the value of the electrical characteristic when a labeled nucleotide is contacted with the polymerase and template parent polynucleotide strand on the tunneling junction with the reference value of the electrical characteristic of the tunneling junction when no labeled nucleotide from the set of nucleotides is bound to the polymerase and template parent strand (“no current”), and upon determining that the electrical characteristic measured in the presence of the labeled nucleotide exceeds the reference value, detecting that the labeled nucleotide has become hybridized to the template parent polynucleotide strand. However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to include instructions in the non-transitory computer readable medium in the system taught by Oldham et al for causing the processor to perform such comparison and detection steps because Oldham et al teach of measuring an electrical characteristic of the tunneling junction both in the presence and in the absence of a labeled nucleotide, wherein the absence of a labeled nucleotide provides a reference “no current” value and the presence of a labeled nucleotide hybridized to a complementary nucleotide on the template parent strand produces a positive electrical characteristic value, thus allowing a determination of a labeled nucleotide being hybridized to the template parent strand when the electrical characteristic measured in the presence of the labeled nucleotide differs from the reference “no current” value.
Oldham et al also fail to teach that the insulating layer of the tunneling junction is sandwiched between and attached to both the first and second electrodes. However, Turner et al teach of a device and a method for sequencing nucleic acids. In the embodiment depicted in Figures 2a-2c, the device comprises a substrate 200 comprising two electrodes 202 and 206 separated by an insulating layer 204 between the electrodes. The insulating layer 204 is sandwiched between and attached to the electrodes 202 and 206. A polymerase enzyme 210 and a nucleic acid templates strand 230 are attached to the insulating layer 204. When a sequencing reaction mixture containing a labeled nucleotide analog 240 having a base complementary to the next position in the template nucleic acid strand 230 is added to the device depicted in Figures 2a-2c of Turner et al, the polymerase enzyme 210 recognizes the nucleotide analog 240 and causes it to hybridize to the complementary base in the template nucleic acid strand 230. The nucleotide analog 240 is labeled with an electrical label 242, and the electrodes 202 and 206 on the device serve to detect an electrical current caused by binding of the labeled nucleotide analog 240 to the complementary template strand 230. The label 242 causes an electrical signal measured at the electrodes to change, thus allowing its presence and identity to be determined. Turner et al teach that the insulating layer 204 sandwiched between and attached to the electrodes 202 and 206 in the device is advantageous since it allows an increase in a distance of the electrodes 202, 206 to ground planes, to other electrodes and to any other conductors which could produce stray electrical signals. See Figures 2a-2c, and paragraphs 0041, 0061-0064 and 0137 in Turner et al.
Based upon a combination of Oldham et al and Turner et al, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to provide the insulating layer of the system for analyzing nucleic acid molecules taught by Oldham et al sandwiched between and attached to both the first and second electrodes rather than as a gap between the electrodes because Turner et al teach that in a similar type of device for analyzing and sequencing nucleic acids using electrical signals to detect hybridization between complementary nucleic acid bases, that it is advantageous to provide an insulating layer sandwiched between and attached to electrodes in the device since this configuration of the insulating layer allows an increase in a distance of the electrodes to ground planes, to other electrodes and to any other conductors which could produce stray electrical signals.
Allowable Subject Matter
Claim 1 would be allowable if rewritten or amended to overcome the rejection(s) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), 2nd paragraph, set forth in this Office action since the closest prior art reference to Oldham et al (WO 2017/189930, submitted in the IDs filed on June 26, 2023), described above, fails to teach or fairly suggest a system for analyzing nucleic acid molecules comprising each of a tunneling junction comprising a first conductor made from a first ferromagnetic material and a second conductor made from a second ferromagnetic material separated by an insulating layer, a polymerase attached to the tunneling junction and connected to a template parent strand of nucleic acids, a power supply in electrical communication with at least the first and second conductors, a set of nucleotides each labeled with a moiety capable of causing a current signal in the tunneling junction, wherein the thickness of the insulating layer is greater than a size of each moiety of each nucleotide in the set of nucleotides, a meter device configured to measure an electrical characteristic through the first conductor and the second conductor via the moiety, and a non-transitory computer readable medium storing instructions that cause a processor to perform the steps recited in instant claim 1.
Claims 2-9, 11-14 and 16-20 would be allowable if rewritten to overcome the rejection(s) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), 2nd paragraph, set forth in this Office action and to include all of the limitations of the base claim and any intervening claims for the same reasons as set forth above.
Response to Arguments
Applicant's arguments filed July 24, 2026 have been fully considered but they are not persuasive.
The previous objection to the specification made in the last Office action mailed on February 25, 2026 has been withdrawn in view of the amendments made to the specification. The previous rejections of the claim under 35 USC 112(b) made in the last Office action have also been withdrawn in view of the amendments made to the claims. However, the amended claims are newly rejected under 35 USC 112(b) for the reasons set forth above, and as necessitated by the amendments made to the claims and the introduction of new claim 21. The previous rejections of the claims under 35 USC 103 as being obvious over Oldham et al, Oldham et al in view of Lindsay et al, and Oldham et al in view of Mandell et al have all been withdrawn in view of the amendments made to the claims and Applicant’s persuasive arguments. New claim 21 is rejected under 35 USC 103 as being obvious over Oldham et al in view of Turner et al (US 2016/0083789, cited in the last Office action mailed on February 25, 2026) for the reasons set forth above.
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 MAUREEN M WALLENHORST whose telephone number is (571)272-1266. The examiner can normally be reached on Monday-Thursday from 6:30 AM to 4:30 PM.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lyle Alexander, can be reached at telephone number 571-272-1254. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from Patent Center. Status information for published applications may be obtained from Patent Center. Status information for unpublished applications is available through Patent Center to authorized users only. Should you have questions about access to the USPTO patent electronic filing system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free).
Examiner interviews are available via a variety of formats. See MPEP § 713.01. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) Form at https://www.uspto.gov/InterviewPractice.
/MAUREEN WALLENHORST/Primary Examiner, Art Unit 1797 September 1, 2026
Prosecution Insights