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 .
Please note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Status
Claims 1-6, 15, 17-24, 27-28, 33-36, 38-39, and 41 are pending and being examined on the merits.
Specification
Applicant’s amendment to the specification to properly note the use of the term “SimpliAmp” (paragraph [0157]) as a trade name or mark used in commerce is acknowledged. However, as noted in the Office Action of 7/1/2025, “SimpliAmp” was not the only trade name or mark used in commerce which appeared in the specification. Other examples include, but are not limited to, “GeneRuler” and “GelRed” (paragraph [0165]), “Viscotek” (paragraph [0169]), and “Biotek Cytation” (paragraph [0172]).
This was not, and is not, a formal objection to the specification and therefore no withdrawal of an objection is necessary.
Claim Objections
The objection to claim 21 is withdrawn in light of Applicant’s amendments.
Maintained Claim Rejections - 35 USC § 103
Claims 1-6, 15, 17-20, 27-28, 34-36, 38-39, and 41 are rejected under 35 U.S.C. 103 as being unpatentable over Pierce et al. (hereinafter “Pierce”; US 7,727,721 B2, cited on IDS submitted on 1/16/2025) in view of Haley et al. (hereinafter “Haley”; bioRxiv, 2018, cited on IDS submitted on 1/16/2025).
Pierce teaches a method for in situ imaging using a hybridization chain reaction involving two hairpin monomers that are fluorescently labelled and an initiator oligonucleotide (Abstract).
Regarding claims 1-6 and 34: Pierce teaches producing a structure comprising a first oligonucleotide hairpin monomer comprising a first toehold, a first duplex stem, and a first hairpin loop, a second oligonucleotide hairpin monomer comprising a second toehold, a second duplex stem, and a second hairpin loop; and an initiator oligonucleotide, wherein hybridization of the initiator oligonucleotide to the first oligonucleotide hairpin monomer results in hybridization of the first oligonucleotide hairpin monomer to the second oligonucleotide hairpin monomer, thereby producing the structure (claim 1 and claim 34; Figure 1A-C and col 2, ln 48-52). Pierce teaches that one or both of the hairpin monomers comprise a fluorescent marker (claim 34a; col 2, 52-53). Pierce teaches that the structure can be employed in a method to detect an analyte in a sample, and that the initiator oligonucleotide comprises an analyte-binding region (claim 34; col 2, ln 42-48). Pierce teaches measuring fluorescence of the sample after contacting to detect the analyte (claim 34; col 3, ln 14-17).
Pierce does not teach wherein the first duplex stem comprises a base-pair mismatch at a position that is proximal to the first toehold and distal to the first hairpin loop, relative to a midpoint of the first duplex stem (claims 1 and 34), wherein the second duplex stem comprises a base-pair mismatch at a position that is proximal to the second toehold and distal to the second hairpin loop, relative to a midpoint of the second duplex stem (claim 4), the position of the base-pair mismatches from the first or second toehold (2 and 5), or inclusion of 2, 3, 4, or 5 base-pair mismatches (claims 3 and 6). However, inclusion of mismatches in duplex regions involved in strand displacement reactions (such as a hybridization chain reaction; HCR) is known in the art, as taught by Haley.
Haley teaches the effect of incorporating single base mismatches in an initial DNA duplex on the displacement rate by an invading strand (Introduction, paragraph 6). Haley tests the effects of the position of the mismatch in relation to a toehold region of the initial duplex and teaches incorporation of mismatches proximal to the toehold region relative to a midpoint of the duplex (claims 1, 4, and 34). Haley teaches incorporation of a mismatch base-pair at a position that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides from the first/second toehold (claims 2 and 5; Figure 2). Haley does not explicitly teach incorporation of 2, 3, 4, or 5 base-pair mismatches (claims 3 and 6). However, it is noted that the courts have found that “where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). See MPEP 2144.05 II. One skilled in the art could readily, through “routine optimization”, determine ideal kinetics of the strand displacement reaction by incorporating more or less base pair mismatches in the duplex stem.
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Pierce with the teachings of Haley. One would be motivated to include mismatches proximal to the toehold of the hairpin monomers given that Haley teaches that proximal (“initial”) mismatches to the toehold “can increase the reaction rate by two orders of magnitude whereas later mismatches have a very small effect” (Introduction, paragraph 6). One would have a reasonable expectation of success given that Haley demonstrates successful strand displacement by an invading strand (similar to an initiator oligonucleotide) into a duplex DNA with a toehold with (similar to the duplex stem and toehold of a hairpin monomer) with base pair mismatches incorporated (Figure 2).
Regarding claims 15, 17, and 35-36: Pierce teaches that the initiator oligonucleotide may be the analyte to be detected in a sample (col 8, ln 26-27) and that the analyte of interest may be mRNA (col 2, ln 58-60).
Regarding claims 18-19 and 39: Pierce teaches that the first hairpin oligonucleotide monomer and the second hairpin oligonucleotide monomer further comprises an additional moiety (“sample is then contacted with at least two fluorescently labeled monomers”; col 3, ln 11-12).
Regarding claims 20 and 41: Pierce teaches that the initiator oligonucleotide further comprises an additional moiety (col 13, ln 4-13). Pierce teaches that the initiator oligonucleotide may comprise an analyte-binding region and that this analyte-binding region comprises an antibody (col 14, ln 65-67 and Figure 9).
Regarding claims 27-28: Pierce teaches an HCR reaction wherein the ratio of the first oligonucleotide hairpin monomer and the second oligonucleotide hairpin monomer to the initiator oligonucleotide is 1:1 or 10:1 (col 19, ln 6-7).
Regarding claim 38: Pierce teaches that the initiator oligonucleotide contains an analyte-binding region that is substantially complementary to the nucleic acid that is the target analyte (col 2, ln 58-62). The “probe” referenced here contains a “target region” that is complementary to the target analyte and “an initiation region” that can initiate HCR and reads on the initiator oligonucleotide (col 2, ln 43-48).
Claims 21-24 are rejected under 35 U.S.C. 103 as being unpatentable over Pierce et al. (hereinafter “Pierce”; US 7,727,721 B2, cited on IDS submitted on 1/16/2025) in view of Haley et al. (hereinafter “Haley”; bioRxiv, 2018, cited on IDS submitted on 1/16/2025) as applied to claims 1-6, 15, 17-20, 27-28, 34-36, 38-39, and 41 above, and further in view of Söderberg et al. (hereinafter “Söderberg”; WO 2015/118029 A1; cited on PTO-892 of 7/1/2025).
The teachings of Pierce in view of Haley are detailed above. Briefly, and relevant to the instantly rejected claims, Pierce in view of Haley teaches a method of HCR in which a structure comprised of two hairpin monomers (one of which contains a base-pair mismatch) are polymerized upon introduction of an initiator oligonucleotide. Pierce in view of Haley teaches that the hairpin monomers may comprise additional moieties, such as fluorescent markers.
Pierce in view of Haley does not teach that the additional moiety is a protein (claim 21), specifically an antibody (claim 22-24). However, appending antibodies to hairpin monomers to be used in an HCR reaction is known in the art, as taught by Söderberg.
Söderberg teaches a method in which hairpin monomers are appended to antibodies, which upon being in close proximity and with addition of an initiator, will perform HCR (claims 21-23; Abstract, pg 20, ln 13-16 and 19-21, and Figure 1). Söderberg provides a working example in which the first and second hairpin monomers are attached to different antibodies (claim 24; pg 59, ln 5-29).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Pierce in view of Haley with the teachings of Söderberg. One would be motivated to attach antibodies as an additional moiety to HCR hairpin monomers given the assertion by Söderberg that by “controlling the interaction of the nucleic acid domains, the assay method or reaction may be allowed to proceed sequentially” and “can significantly improve the sensitivity and specificity of the assay” (pg 7, ln 5-7). One would have a reasonable expectation of success given that Söderberg demonstrates a successful generation of HCR products upon attachment of hairpin monomers to antibodies (pg 59, ln 5-29).
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Pierce et al. (hereinafter “Pierce”; US 7,727,721 B2, cited on IDS submitted on 1/16/2025) in view of Haley et al. (hereinafter “Haley”; bioRxiv, 2018, cited on IDS submitted on 1/16/2025) as applied to claims 1-6, 15, 17-20, 27-28, 34-36, 38-39, and 41 above, and further in view of Li et al. (hereinafter “Li”; Journal of the American Chemical Society, 2012; cited on PTO-892 of 7/1/2025).
The teachings of Pierce in view of Haley are detailed above. Briefly, and relevant to the instantly rejected claims, Pierce in view of Haley teaches a method of HCR in which a structure comprised of two hairpin monomers (one of which contains a base-pair mismatch) are polymerized upon introduction of an initiator oligonucleotide.
Pierce in view of Haley does not teach a method further comprising contacting the structure with a termination oligonucleotide. However, contact of an HCR structure with a termination oligonucleotide is known in the art, as taught by Li.
Li teaches a method in which a hybridization chain reaction structure (2 hairpin monomers plus a trigger/initiator oligonucleotide) is used to initiate catalyzed hairpin assembly (pg 13918, col 2, paragraph 1; Figure 1). Li teaches that a “Lock” oligonucleotide may be added to terminate the reaction (pg 13919, col 2, paragraph 2; Figure 3). The “Lock” oligonucleotide reads on termination oligonucleotide.
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Pierce in view of Haley with the teachings of Li. One would be motivated to add a terminator oligonucleotide given the assertion by Li that this “allows timely termination of the HCR” and thus allows control of the reaction procession. One would have a reasonable expectation of success given that Li demonstrates successful use of the Lock oligonucleotide to terminate the HCR reaction.
Response to Remarks
In the Remarks of 12/31/2025 (“Remarks”), Applicant traverses all rejections as presented in the Office Action of 7/1/2025. Applicant's arguments filed 12/31/2025 have been fully considered but they are not persuasive for the following reasons.
Applicant argues on page 10 of Remarks that Haley “discloses a fundamentally different system and purpose than the claimed methods”. Applicant argues that “Haley’s system involves a simple duplex with an invading strand, not hairpin monomers used in a hybridization chain reaction” (pg 10 of Remarks). In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). The teachings of Haley are considered analogous art, in that Haley teaches the effects of mismatch placement on toehold-mediated strand displacement kinetics, which is directly applicable to the toehold-mediated strand displacement that is required for hybridization chain reactions as taught by Pierce.
Applicant argues on page 10 that Haley teaches “the opposite of what is presently claimed”. However, while Haley does teach a benefit of including mismatches in a duplex strand away from the toehold, Haley also teaches benefits to reactions rates by including mismatches near the toehold, specifically at 3 base pairs from the toehold/beginning of the duplex. These advantages include 1) increasing the reaction rate by two orders of magnitude (1.1 The dependence of displacement rate on mismatch position, paragraph 3) and 2) kinetically favors strand invasion by the invading strand when the mismatch is closer to said invading strand at the beginning of the reaction (1.3 Demonstrating and exploiting hidden thermodynamic driving in a pulse-generating circuit). A given course of action often has simultaneous advantages and disadvantages, and this does not necessarily obviate motivation to combine. See id. at 1349 n. 8 (“The fact that the motivating benefit comes at the expense of another benefit, however, should not nullify its use as a basis to modify the disclosure of one reference with the teachings of another. Instead, the benefits, both lost and gained, should be weighed against one another.”). reference might accurately discredit another.’ In re Young, 927 F.2d 588, 591 (Fed.Cir.1991).”
In response to applicant's argument on page 10 of Remarks that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., kinetic differentiation between initiation and propagation) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). This also applies to the argument on page 11 of Remarks that “Haley does not teach or suggest how a mismatch affects propagation rates in HCR”. This is not a feature that is claimed in the current invention. Haley teaches that initial toehold-mediated displacement rates can be significantly increased by the incorporation of mismatches in a duplex strand when proximal to the toehold. Effects on sequential strand displacement events and kinetic differentiation of imitation versus propagation are not features claimed in the current invention.
For these reasons, and the rationales provided in the 103 rejections above, the rejections are maintained.
Conclusion
THIS ACTION IS MADE FINAL. 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 KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683 /ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683