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 Status
Claims 1-12 and 14-21 are pending and under examination. Claim 1 and 14 are independent claims. No claims have been amended, cancelled, or withdrawn.
Response to Arguments
Applicant's arguments filed 06/18/2026 have been fully considered but they are not persuasive.
Applicant’s “No Motivation to Combine” Argument
Applicants argues that “there would be no motivation for one of skill in the art to combine the teachings of Raz and Allawi,” asserting that Raz’s hairpin primers “rely solely on the use of isotropical complementary base-pairing in the stem domain” and that Raz “emphasizes that hairpin stability derives from canonical intramolecular complementarity,” such that “there is no suggestion, express or implied, anywhere in Raz to incorporate non-canonical G-T or G-U wobble pairs in the hairpin stems.” (see Remarks at pg. 5; citing Raz [0049]-[0051], [0054], [0072]). This characterization of Raz is not accurate.
First, Raz expressly identifies “the number of mismatches or bulges” as one of the factors determining hairpin stem stability, alongside stem length and base composition: “The stability of a hairpin is determined for example by its length, the number of mismatches or bulges, and the base composition of the intramolecular paired region” (see Raz [0072]). Raz thus does not teach that hairpin stability derives solely from perfect canonical complementarity, as Applicant contends. To the contrary, Raz expressly identifies mismatches as a design variable affecting stem stability, and further expressly teaches that base-pair composition can be deliberately selected to modulate that stability: “the stem structure of the hairpin can comprise one or more additional GC base pairings as compared to AT base pairings in the stem structure, to improve the stability of the hairpin” (see Raz [0072]). A person of ordinary skill in the art reading Raz would therefore have understood that hairpin stem stability is governed by identifiable, deliberately selectable sequence level variables, including the presence of mismatches, and Raz’s own primer architecture depends critically on precise, tunable control of that stability relative to the reaction’s annealing temperatures (see Raz [0072]).
Second, Raz’s own disclosure does not require perfect Watson-Crick complementarity even in the specific stem-to-stem relationship between the target specific and universal primer hairpins. Raz expressly states that the universal hairpin primers “may include one or two mismatches” in their otherwise complementary relationship to the target-specific hairpin primer’s 5’ region (see Raz [0074]). Applicant’s characterization of Raz as relying on strict canonical complementarity is therefore inconsistent with Raz’s own express disclosure of a primer architecture that already tolerates mismatches.
Given Raz’s express recognition that mismatches are a known variable affecting hairpin stem stability, and Raz’s express teaching that hairpin stem stability relative to the reaction’s annealing temperature is “an important design parameter” for primer function (see Raz [0072]), a person of ordinary skill in the art would have been motivated to look to the art for known means of introducing a specific, well-characterized mismatch into a hairpin stem in order to further tune that stability. Allawi supplies exactly that, a specific, well-characterized, quantitatively predictable class of mismatch (G-T/G-U wobble pairing) with published thermodynamic parameters directly applicable to that purpose (see Allawi Abstract, Tables 1, 4-5). The combination of Raz’s express teaching that mismatches are a stability determining variable with Allawi’s specific quantified means of introducing and predicting the effect of one particular class of mismatch is a combination of known elements according to their established functions, yielding no more than a predictable result. See KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 398, 82 USPQ2d 1385 (2007) “The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.”
Applicant’s “No Reasonable Expectation of Success” Argument
Applicant argues that the effect of a G-T (or G-U) mismatch on duplex stability is “not predictable and cannot be treated as a simple parameter for routine optimization” citing Allawi’s disclosure that the thermodynamic contribution of a single G-T mismatch ranges from approximately +1.05 kcal/mol (AGA/TTT) to -1.05 kcal/mol (CGC/GTG) depending on sequence context (see Remarks pg. 6, Allawi Abstract). This argument is not persuasive because it conflates context-dependence with unpredictability. Allawi’s central finding, expressly stated in the Abstract and developed throughout the Results and Discussion section, is that a nearest-neighbor thermodynamic model predicts the free energy, enthalpy, entropy, and melting temperature contributions of G-T mismatches with average deviations of only 5.1%, 7.5%, 8.0%, and 1.4 °C, respectively (see Allawi Abstract, “Applicability of the Nearest-Neighbor Model to G-T Mismatches”, pg. 10590-10592). That the sing and magnitude of a given G-T mismatch’s contribution varies with its local sequence context does not render the effect unpredictable, to the contrary, Allawi’s data establishes that the effect is reliably and quantitatively predictable once sequence context is specified, using nothing more than routine application of Allawi’s own published nearest-neighbor parameters (see Allawi Tables 4-5).
This is confirmed by the state of the art as reflected in publicly available nucleic acid folding and hybridization prediction software that predates the effective filing date of the present application. The DINAMelt/UNAFold web server, the very tool the Applicant’s own specification identifies as the source of every melting-temperature value reported in the specification (see Specification at [0049]), incorporates, as part of its standard single-nearest neighbor parameter set, the thermodynamic parameters published by Allawi and SantaLucia, including G-T mismatch parameters of the Allawi reference applied in this rejection. See Zuker, M., “Mfold web server for nucleic acid folding and hybridization prediction” Nucleic Acids Research, Volume 31, Issue 13, 1 July 2003, Pages 3406–3415 (identifying Allawi and SantaLucia among the references for the single-mismatch parameters incorporated into the Mfold/UNAfold webserver) and Markham, N.R. & Zucker, M., “DINAMelt web server for nucleic acid melting prediction” Nucleic Acids Research, Volume 33, Issue suppl_2, 1 July 2005, Pages W577–W581 (the reference Applicant’s own specification cites at [0049] as the basis for its Tm-calculations methodology).
Applicant’s own specification relies on this software, built directly on Allawi’s mismatch thermodynamic data, to calculate and confirm the claimed Tm-as1, Tm-ts, and Tm-as1/Tm-ts differential values throughout the application. This is itself evidence that a person of ordinary skill in the art, as of the effective filing date, possessed both a motivation and a reasonable expectation of success in calculating and applying G-T mismatch thermodynamics to a primer hairpin stem, since this is precisely the calculation the field’s standard, publicly available software performed as a matter of routine practice. Applicant cannot rely on Allawi’s thermodynamic framework, via a software tool built on Allawi’s own published parameters, to design and validate the claimed primers, while simultaneously arguing that a person of ordinary skill in the art would have lacked a reasonable expectation of success in applying that same, publicly available framework for that same purpose. See MPEP 2143(I)(E); MPEP 2144.05(II).
Applicant’s Argument that Allawi’s Data Does Not Extend to Hairpin Structures
Applicant further argues that Allawi is inapplicable because Allawi’s sequences were “designed to exclude hairpin-forming structures” and that Allawi’s data therefore says nothing about G-T mismatches behavior within a hairpin stem (see Remarks pg. 6). This argument is not persuasive. The very software identified above, which applies Allawi’s nearest-neighbor mismatch parameters as its standard mismatch energy set, uses those same parameters to compute minimum free energy intramolecular (hairpin) secondary structs, not solely linear intermolecular duplexes. This reflects a well understood premise underlying the nearest-neighbor model generally, that local base-pair stacking thermodynamics are determined by local sequence context, independent of the larger-scale topology in which that local context occurs. Accordingly, it was well within the ordinary skill in the art, and a matter of routine, well-established practice reflected in publicly available software, prior to the effective filing date, to apply Allawi’s published G-T mismatch nearest-neighbor parameters to a hairpin stem context, notwithstanding that Allawi’s own experimental measurements were performed on sequences designed to avoid hairpin formation for purposes of obtaining clean two-state melting data.
Applicant’s Hindsight Argument
Applicant argues that “one of skill in the art would not have arrived at the claimed invention based on reading of Raz and Allawi without the benefit of hindsight derived from the knowledge of the present application,” and further asserts that “the present application made a counterintuitive discovery”, namely that G-T mismatches, “while reducing thermodynamic stability in a symmetric duplex context, creates an exploitable asymmetry between hairpin primer and template complement that actually improves amplification performance,” citing paragraph [0007] of the instant specification (see Remarks pg. 6). This argument is not persuasive.
The motivation to combine Raz and Allawi articulated in this rejection is drawn entirely from the teachings of Raz and Allawi themselves. Specifically, Raz’s own express identification of hairpin stem stability, and the presence of mismatches, as a design parameter governing primer function (see Raz [0072]), and Allawi’s own express teaching of a specific, well-characterized, and quantitatively predictable means of tuning duple region stability through G-T/G-U wobble pairing (see Allawi Abstract, Tables 1, 4-5). No aspect of this rejection’s rationale is drawn from, or requires reference to, Aplicant’s specification. It is well settled that “[a]ny judgment on obviousness is in a sense necessarily a reconstruction based on hindsight reasoning, but so long as it takes into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant’s disclosure, such a reconstruction is proper." In re McLaughlin, 443 F.2d 1392, 1395, 170 USPQ 209, 212 (CCPA 1971); MPEP 2145(X)(A). Because the motivation and reasonable expectation of success relied upon here derive solely from Raz and Allawi, and are further corroborated by the standard, publicly available nucleic acid folding software discussed above (which predates the effective filing date and was not derived from Applicant’s disclosure), the rejection does not rely on impermissible hindsight.
With respect to Applicant’s assertion of a “counterintuitive discovery” reflected in the specification at paragraph [0007], this is unsupported by evidence of record. A specification’s own characterization of its results as counterintuitive or unexpected is not evidence and cannot, without more, rebut a prima facie case of obviousness. Arguments presented by applicant cannot take the place of evidence in the record. See In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984); In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965); In re Geisler, 116 F.3d 1465, 43 USPQ2d 1362 (Fed. Cir. 1997) ("An assertion of what seems to follow from common experience is just attorney argument and not the kind of factual evidence that is required to rebut a prima facie case of obviousness."). To rebut a prima facie case of obvious with evidence of unexpected results, an applicant must submit factual evidence. See MPEP 716.02. No such evidence is currently of record.
For at least the reasons listed above, the incorporation of at least one G-T or G-U wobble pairing into the hairpin stem of Raz’s primers, for the purpose of adjusting the stems thermodynamic stability by a specific, calculable, and reliably predictable amount would have been well within the skill of a person of ordinary skill in the art at the time of filing. Raz itself identifies mismatches as a stability determining design variable and teaches that stem stability is an important tunable parameter. Allawi supplies a specific, well-characterized, and quantitatively predictable class of mismatch directly suited to that purpose. The motivation and reasonable expectation of success underlying this rejection are drawn entirely from Raz and Allawi and the state of the art, not from Applicant’s disclosure and Applicant has not presented evidence of record sufficient to establish unexpected results. The rejection of claims 1-12 and 14-21 under 35 U.S.C. 103 as being unpatentable over Raz in view of Allawi is maintained.
Conclusion
No claim is allowed.
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.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/ Primary Examiner, Art Unit 1681
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