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 . 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.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 25 May, 2026 has been entered.
Election/Restrictions
Applicants elected group I and SEQ ID 15 without traverse in the reply filed on 29 July, 2025.
Claims Status
Claims 22-32 are pending.
Claims 22-32 are new.
Claims 26-31 have been withdrawn due to an election restriction requirement.
Withdrawn Objections
The objection to claim 14 due to improper markup is hereby withdrawn due to amendment
The objection to claim 4 due to duplicate claims is hereby withdrawn due to amendment.
Withdrawn Rejections
The rejection of claims 3-5, 11, 14, and 15 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph due to lack of antecedent support for a conjugation site is hereby withdrawn due to amendment.
The rejection of claim 2 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite due to uncertainty as to the number of conjugation sites is hereby withdrawn due to amendment.
The rejection of claim 14 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph due to multiple percent identities is hereby withdrawn due to amendment.
The rejection of claims 2-5 and 11 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form is hereby withdrawn due to amendment.
The rejection of claim(s) 14 under 35 U.S.C. 103 as being unpatentable over Merriman et al (US 20170044605, cited by applicants) in view of Guo et al (Mol. Biosyst. (2017)13 p598-606) and Chiu et al (Nanoscale (2010) 2 p927-930) is hereby withdrawn due to amendment.
Maintained/Modified Rejections
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.
first rejection
Claim(s) 22-25 are rejected under 35 U.S.C. 103 as being unpatentable over Merriman et al (US 20170044605, cited by applicants) in view of Guo et al (Mol. Biosyst. (2017)13 p598-606), Chiu et al (Nanoscale (2010) 2 p927-930), Rohl et al (PNAS (1999) 96 p3682-3687), Stein et al (US 20170315114), To et al (PNAS (2015) 112(11) p3338-3343), Cesaratto et al (J. Biotech. (2015) 212 p159-166), and Strop et al (Chem. Biol. (2013) 20 p161-167).
Merriman et al discuss electronic sensors comprising two electrodes separated by a sensor gap, coupled by a biopolymer bridge and a probe that can interact with a target molecule (abstract). The bridge molecule can self assemble on the electrodes (paragraph 11). These electrodes can be operatively connected to a circuit to detect a change of an electrical property (paragraph 42). The bridge is sized to span the sensor gap using precise molecular subunits (paragraph 52), such as helix turns (paragraph 57). The bridge molecule can be made of amino acid motifs known to form a helix, such as SEQ ID 8 (EAAAR), identical with SEQ ID 1 of the examined claims, which can be modified to have a conjugation site, such as lysine, to bind to the probe molecule (paragraph 61). These can have a metal binding sequence that binds strongly to the metal contacts, such as gold, palladium, or platinum, with sequences such as SEQ IDs 3-5, with C-terminal Ser residues (Gly/Ser rich linker). The probe can be a polymerase (paragraph 65). The bridge molecule itself can be a probe molecule as well (paragraph 67).
The difference between this reference and the examined claims is that this reference describes a sequence somewhat different than SEQ ID 15 of the examined claims.
Guo et al discuss linker lengths (title). In fusion proteins, such as the sequence of Merriman et al, linkers between the various segments can improve folding and stability, enhance expression, and elevate biological activity (p598, 1st column, 1st paragraph). Length has a direct impact on the activity of the fusion protein (p598, 1st column, 1st page). Among the most common linkers used are (Gly-Ser-Gly)n (p598, 2nd column, 1st paragraph). This reference discusses applicant’s elected linker, stating it is one of the most common linkers used.
Chiu et al discusses peptides involved in palladium nanoparticle synthesis (title). Phage display finds a sequence QQSWIPS, which binds specifically to the metal surface (p927, 2nd column, 2nd paragraph). Combined with a teaching of Merriman et al of palladium electrodes and using sequences that bind to those electrodes, this renders obvious using the sequence of Chiu et al.
Rohl et al discuss alanine in the context of helices (title). Alanine has a propensity to form helices (p3682, 2nd column, 2nd paragraph). While more alanines will more strongly promote helical structure, even a single one will promote that tertiary structure (fig 2, p3684, 2nd column, top of page). This reference discusses the propensity of alanines to promote a helix.
Stein et al discusses biosensors (title). A protease activity can be detected by the protease digesting a conducting substrate, changing conductivity of the construct (paragraph 162). This reference teaches using a protease sensitive substrate for electrochemical detection of a protease.
To et al discusses a protease sensor (title). As proof of concept, the TEV cleavage sequence was used in their protease scaffold (p3339, 1st column, 2nd paragraph). Cesaratto et al teaches that the substrate for this protease is ENLYFQ-G/S (p159, 1st column, 2nd paragraph).
Strop et al discuss how the location of conjugation affects stability of constructs (title). In the context of antibody-drug conjugates, the location of conjugation significantly affects stability (abstract). Conjugation usually is via Cys or Lys residues (p161, 1st column, 1st paragraph). Engineered cysteines allow a practitioner in this field to conjugate at a specific location (p161, 2nd column, 1st paragraph). Note that the reference discusses embodiments that use Cys residues for conjugation as conventional (p163, 2nd column, 2nd paragraph). This reference discusses using Cys residues for conjugation.
Therefore, it would be obvious to use the linkers of Guo et al between the segments of Merriman et al, to improve folding, stability, activity, and enhance expression. As this is one of the most commonly used linkers, an artisan in this field would attempt this modification with a reasonable expectation of success.
Furthermore, it would be obvious to use the metal binding peptide of Chiu et al to specifically bind to the palladium electrodes of Merriman et al. As Merriman et al functionally discuss peptides that bind to these electrodes, an artisan in this field would attempt this modification with a reasonable expectation of success.
In addition, it would be obvious to add one or more alanines to either side of the helix of Merriman et al, to promote folding into a helical conformation, as described by Rohl et al. As this reference shows that Ala is a helix forming residue, an artisan in this field would attempt this modification with a reasonable expectation of success.
Plus, it would be obvious to add one or more protease sequences to the polypeptide of Merriman et al, to allow for detection of a protease. As Merriman state that the bridge molecule can also be a probe, an artisan in this field would attempt this modification with a reasonable expectation of success.
Furthermore, it would be obvious to use the TEV protease sequence of To et al as a proof of principle. As this is a very robust protease, an artisan in this field would attempt this sequence with a reasonable expectation of success.
In addition, it would be obvious to use a Cys residue for conjugation of the probe molecule of Merriman et al), rather than the Lys reside of that reference, as a simple substitution of one known element (the Lys conjugation of Merriman et al) for another (the Cys conjugation of Strop et al) yielding expected results (conjugation of the probe molecule). As Strop et al discusses conjugation via Cys as conventional, an artisan in this field would attempt this modification with a reasonable expectation of success.
Finally, as Strop et al teaches that the location of the conjugation affects stability, it would be obvious to try the various locations in the molecule to maximize stability. As this would attempt numerous positions in the molecule, an artisan in this field would attempt this process with a reasonable expectation of success.
Applicant’s elected species, SEQ ID 15, is three copies of SEQ ID 16 (obvious by Chiu et al), separated by GSG linkers (obvious by Guo et al) on either side of the sequence, with the body of the sequence a helix made of repeating motifs of SEQ ID 1 (obvious by Merriman et al), with an alanine on either side of that sequence (obvious by Rohl et al), a protease sequence between two of the binding sequences (obvious by To et al and Stein et al), with a Cys residue in the center to conjugate the polymerase to (obvious by Strop et al). In other words, this is merely a combination of known elements yielding expected results, rendering obvious claims 2-5 and 11.
response to applicant’s arguments
Applicants argue that SEQ ID 15 has a K to R mutation compared to the sequence of Merriman et al, that the sequences of Gou et al are entirely different than those of Merriman et al, that the alanine stabilization of a helix taught by Rohl et al would not be expected to apply to the sequence of Merriman et al, that there is no coherent reason why a person of skill in the art would look to these references, that none of the cited references recite the sequence ENLYFGQ, that the references are from disparate technical domains, that there are too many cited references to render the claims obvious, there is no reasonable expectation of success, that the Arg residues in the Arg residues of the examined claims would be expected to aggregate more than the Lys residues of Merriman et al, mention improper obvious to try, and argue hindsight reasoning,
Applicant's arguments filed 25 May, 2026 have been fully considered but they are not persuasive.
Applicants argue that SEQ ID 15 has an K to R mutation compared to the sequence of Merriman et al. This is an error in the rejection and has been corrected.
Applicants argue that the sequences of Gou et al are entirely different than those of Merriman et al, so the linker would be expected to behave differently. Applicants have pointed to no section of Gou et al that limits the findings to the specific sequences used in the reference; indeed, the discussion clearly is more generic than that (p598, 1st column, 1st paragraph). Applicants have not provided any evidence that would persuade a person of skill in the art that the linkers of that reference would be ineffective in the application of Merriman et al. Applicants have provided no logical reasoning to this effect. In essence, applicants have pointed to differences between Gou et al and the examined claims and stated that they are too great. This is not sufficient to overcome the rejection.
Similarly, applicants argue that the helix stabilization by alanine taught by Rohl et al would not be expected to work with the structures of Merriman et al. Again, this is argument is merely a list of differences between the two references with a conclusory statement that the differences are too great, even though the reference clearly is intended to be more general than the specific examples given (abstract).
Applicants argue that there is no coherent reason why a person of skill in the art would look at these references. This is an argument of non-analogous art, which was answered previously.
Applicants argue that none of the cited references give the TEV protease sequence ENLYFGQ. That sequence is not found in SEQ ID 15; applicants may be arguing that the sequence ENLYFQG, the TEV protease cleavage site, is missing from the prior art. However, as noted in the rejection, this sequence is taught by To et al.
Applicants argue that cited references are from disparate technical domains. Again, this is an argument of non-analogous art, which has been previously answered.
Applicants argue that there are too many cited references to render the claims obvious. This argument has been previously presented and the response is of record.
Applicants argue that there is no reasonable expectation of success because the Arg residues of SEQ ID 15 would be considered much more likely to form aggregates than the Lys residues of Merriman et al. The argument is that the charge on the Arg residue is more diffuse than the charge on the Lys residue, so it would be more likely to aggregate, presumably by charge charge interactions with the Glu residues. Applicants have not explained how the softer Arg residue would be more likely to aggregate, nor is it immediately obvious. At distances large compared to the size of the charged area, the attraction would be expected to be the same for either – simple coulombic attraction. At closer distances, the Lys would be expected to have a stronger attraction to the Glu residues due to the more concentrated charge on that ion. Alternatively, by HSAB theory, the hard amine ion in the Lys residue would be more strongly attracted to the hard carboxylate of the Glu residue than the softer Arg side chain. In any event, Merriman et al explicitly discusses sequences with an Arg residue in that position, discussed in the rejection. That gives a reasonable expectation of success.
Applicants mention improper obvious to try. It is not clear how this argument relates to the rejection; the only obvious to try rationale used in the rejection relates to the location of the Cys residue. The prior art clearly shows that this is a result oriented variable, with only one variable (the position of the Cys in the sequence) being modified. This does not fit the description of applicants of an improper obvious to try, with many variables.
Finally, applicants argue hindsight reasoning. The test for hindsight reasoning is if the rejection does not include knowledge gleaned only from the applicant's disclosure, see In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). While applicants have expounded on why they believe the rejection is based on hindsight, nowhere is there any discussion of portions of the rejection that are absent from the cited references.
second rejection
Claim(s) 22-25 and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Merriman et al (US 20170044605, cited by applicants) in view of Guo et al (Mol. Biosyst. (2017)13 p598-606), Chiu et al (Nanoscale (2010) 2 p927-930), Rohl et al (PNAS (1999) 96 p3682-3687), Stein et al (US 20170315114), To et al (PNAS (2015) 112(11) p3338-3343), Cesaratto et al (J. Biotech. (2015) 212 p159-166), Strop et al (Chem. Biol. (2013) 20 p161-167), and Pease (Electronic design library, 2001).
Merriman et al discuss electronic sensors comprising two electrodes separated by a sensor gap, coupled by a biopolymer bridge and a probe that can interact with a target molecule (abstract). The bridge molecule can self assemble on the electrodes (paragraph 11). These electrodes can be operatively connected to a circuit to detect a change of an electrical property (paragraph 42). The bridge is sized to span the sensor gap using precise molecular subunits (paragraph 52), such as helix turns (paragraph 57). The bridge molecule can be made of amino acid motifs known to form a helix, such as SEQ ID 9 (EAAAK), identical with SEQ ID 1 of the examined claims, which can be modified to have a conjugation site, such as lysine, to bind to the probe molecule (paragraph 61). These can have a metal binding sequence that binds strongly to the metal contacts, such as gold, palladium, or platinum, with sequences such as SEQ IDs 3-5, with C-terminal Ser residues (Gly/Ser rich linker). The probe can be a polymerase (paragraph 65). The bridge molecule itself can be a probe molecule as well (paragraph 67).
Guo et al discuss linker lengths (title). In fusion proteins, such as the sequence of Merriman et al, linkers between the various segments can improve folding and stability, enhance expression, and elevate biological activity (p598, 1st column, 1st paragraph). Length has a direct impact on the activity of the fusion protein (p598, 1st column, 1st page). Among the most common linkers used are (Gly-Ser-Gly)n (p598, 2nd column, 1st paragraph). This reference discusses applicant’s elected linker, stating it is one of the most common linkers used.
Chiu et al discusses peptides involved in palladium nanoparticle synthesis (title). Phage display finds a sequence QQSWIPS, which binds specifically to the metal surface (p927, 2nd column, 2nd paragraph). Combined with a teaching of Merriman et al of palladium electrodes and using sequences that bind to those electrodes, this renders obvious using the sequence of Chiu et al.
Rohl et al discuss alanine in the context of helices (title). Alanine has a propensity to form helices (p3682, 2nd column, 2nd paragraph). While more alanines will more strongly promote helical structure, even a single one will promote that tertiary structure (fig 2, p3684, 2nd column, top of page). This reference discusses the propensity of alanines to promote a helix.
Stein et al discusses biosensors (title). A protease activity can be detected by the protease digesting a conducting substrate, changing conductivity of the construct (paragraph 162). This reference teaches using a protease sensitive substrate for electrochemical detection of a protease.
To et al discusses a protease sensor (title). As proof of concept, the TEV cleavage sequence was used in their protease scaffold (p3339, 1st column, 2nd paragraph). Cesaratto et al teaches that the substrate for this protease is ENLYFQ-G/S (p159, 1st column, 2nd paragraph).
Strop et al discuss how the location of conjugation affects stability of constructs (title). In the context of antibody-drug conjugates, the location of conjugation significantly affects stability (abstract). Conjugation usually is via Cys or Lys residues (p161, 1st column, 1st paragraph). Engineered cysteines allow a practitioner in this field to conjugate at a specific location (p161, 2nd column, 1st paragraph). Note that the reference discusses embodiments that use Cys residues for conjugation as conventional (p163, 2nd column, 2nd paragraph). This reference discusses using Cys residues for conjugation.
As noted above, these rejections render obvious claims 22-25.
The difference between these references and the remaining claim is that this reference does not specify a transimpedance amplifier.
Pease discusses transimpedance amplifiers (title). These are quite useful to amplify a signal from a sensor (3d page, 1st paragraph). This reference discusses using transimpedance amplifiers to amplify a signal from a sensor.
Therefore, it would be obvious to use the transimpedance amplifier of Pease to amplify the signal of the sensor of Merriman et al. As Merriman et al discusses additional circuitry in their system for similar purposes, an artisan in this field would attempt this modification with a reasonable expectation of success.
response to applicant’s arguments
Applicants have presented the same arguments for all rejections under this statute, which was answered above.
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.
Claims 22-25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 3-5 of copending Application No. 18/843,280 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the competing claims anticipate the examined claims.
Competing claim 1 describes a sensor comprising a bridge molecule between an electrode with a probe molecule connected to the bridge molecule, while claim 3 specifies a conjugation site for the probe. Competing claim 4 specifies that the probe is a polymerase, while competing claim 5 specifies a Markush group including SEQ ID 18, which comprises SEQ ID 15 of the examined claims. While the competing claims only mention one electrode, duplication of parts is not a patentable distinction (MPEP 2144.03(VI)(B)).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
response to applicant’s arguments
Applicants argue that duplication of parts is too large a change for this to be obvious.
Applicant's arguments filed 25 May, 2026 have been fully considered but they are not persuasive.
Applicants argue that going from one electrode to two electrodes is too great a difference to be obvious as duplication of parts. However, in both cases, the same sequence is being used for an electrical measurement to detect the same reactant. The principle of operation is the same, the binding and detection system is the same.
New Rejections
Improper Markush
Claim 25 is rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of claim 25 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: except for SEQ IDs 15 and 21, there is no sequence identity between the different sequences of the claims. This means that there is no common sequence, and hence, no single structural similarity.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRED REYNOLDS whose telephone number is (571)270-7214. The examiner can normally be reached M-Th 9-3:30.
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/FRED H REYNOLDS/Primary Examiner, Art Unit 1658
