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 .
Election/Restrictions
Applicant's election with traverse of the invention of Group I and the particular dye that is Dy360XL in the reply filed on 01/20/2026 is acknowledged. In light of the traversal set forth in the reply, and the Examiner’s search of the elected invention, the restriction requirement and the species election requirements set forth in the papers of 11/19/2025 are withdrawn.
Improper Multiple Dependent Claims
Claims 6-9 and 15-18 are objected to under 37 CFR 1.75(c) as being in improper form because a multiple dependent claim cannot depend from any other multiple dependent claim. See MPEP § 608.01(n). Accordingly, the claims 6-9 and 15-18 have not been further treated on the merits.
Claim Rejections - 35 USC § 112 - Indefiniteness
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 4, 5, 13 and 15 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.
The rejected claims contain trademark/trade names, including: Alexa Fluor, Cascade Yellow, CF, Chromeo, Dapoxyl, Dylight, Krome Orange, Pulsar, VioGreen, Pacific Orange. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe dyes and, accordingly, the identification/description is indefinite.
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.
Claim(s) 10-13 are is/are rejected under 35 U.S.C. 103 as being unpatentable over Chakravorty et al (2017) as cited on the IDS of 02/24/2026 incuding the Supplementary Information in view of Hiddessen et al (US PG Pub 2018/0147573).
Relevant to the limitations of claim 10, Chakravorty et al a method for the multiplexed detection of target nucleic acids (e.g.: p.194; Fig 3) (relevant to step (a)) using methods comprising the amplification of the target nucleic acids using primer pairs for each target, hybridization of the resulting amplicons to probes comprising fluorescent dyes and quencher moieties, and measuring a detectable signal from the dye labels (e.g.: p.186; Fig. 3; Fig. 4; Supplementary Tables 1 and 2) (relevant to (a)(i)-(a)(iii) of claim 1). Further relevant to claim 10, Chakravorty et al teaches that the utility of the multiplex assay is expanded by using combinations of small stokes shift (SSS) and large stokes shift (LSS) dye labels where the labels have similar excitation/absorption peak maxima and different emission peak maxima (e.g.: p.185 - Large Stokes-shift fluorescent chemistries increase usable detection channels; Fig. 1 “overlapping of the excitation maxima”).
Chakravorty et al does not teach separating dyes and quenchers of probes using the 5’ to 3’ nuclease activity of a polymerase during an extension step of a polymerase chain reaction (relevant to step (b) of claim 10), or the measuring of detectable signals from dyes multiple times after repeated amplification cycles (relevant to steps (c), (d) and (e) of claim 10). Chakravorty et al does not teach specific differences in emission peak maxima of the dyes (e.g.: at least 80nm (claim 10), greater than 80nm (claim 11), greater than 100nm (claim 12)), or the particular dye that is Pulsar 650 (claim 13). But such aspects of multiplexed detection of nucleic acids were known in the prior art and art taught by Hiddessen et al.
Hiddessen et al teaches reagents and methods for the detection of target nucleic acids. Relevant to the instantly rejected claims, Hiddessen et al teaches assays that can be multiplexed and can include 5’-nuclease assays (e.g.: para 1155-1157) and quenchers (e.g.: Fig 123; para 1074) that are cleaved by the nuclease activity (e.g.: para 859). Relevant to steps (c), (d) and (e), the reference teaches the detection of target dependent fluorescence in a real-time PCR assay in which amplicon formation is measured during the reaction, such as after completion of one or more thermal cycles prior to the final thermal cycle of the reaction (e.g.: para 197). Hiddessen et al specifically teaches (e.g.: Fig. 128; para 1100) a combination of dyes that include FAM (a SSS dye) and PULSAR 650 (a LSS dye) (relevant to claim 13) which are excited at similar maxima (460-480 nm) and have different emission maxima (i.e: 520 nm for FAM; 650 for PULSAR 650) (an emission difference of 130nm; relevant to claim 10, 11 and 12) each paired with a quencher.
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have incorporated the teachings of Chakravorty et al, including the multiplexed detection of target nucleic acids using primers for amplification of a target nucleic acid and dye/quencher labeled probes with spectrally overlapping dyes for amplicon detection, into the methods of Hiddessen et al including multiplexed detection of FAM and PULSAR 650 labeled probes via a 5’-nuclease assay. The skilled artisan would recognize that the detection methods of Hiddessen et al would be the simple substitution of one know methodology (a 5’-nuclease assay) for another (the molecular bacon assay of Chakravorty et al) with predictable results.
Claim(s) 13 and 14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chakravorty et al (2017) as cited on the IDS of 02/24/2026 including the Supplementary Information in view of Hiddessen et al (US PG Pub 2018/0147573) as applied to claims 10-13 above, and further in view of Mueller et al (US PG Pub 2017/0002398.
Chakravorty et al in view of Hiddessen et al renders obvious methods comprising detection target nucleic acids using a 5’-nuclease real-time PCR method and LSS and SSS dyes with similar adsorption peak maxima and different emission peak maxima.
Chakravorty et al in view of Hiddessen et al does not teach the particular dye that is Chromeo 494, as recited in claims 13 and 14.
However, the use of Chromeo 494 as label for nucleic acids, and the absorption and emission peak maxima of Chromeo 494 were known in the prior art and are taught by Mueller et al (e.g.: p.6 – Claim 7; p.5 – Table 1).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have used the dye Chrome 494 in the methods rendered obvious by Chakravorty et al in view of Hiddessen et al. Where the prior art teaches the absorption and emission maxima of Chromeo 494, and teaches that the dye is suitable for use in real-time PCR methods, the use of Chromeo 494 and pairing it with a dye that has a similar absorption maximum and different emission maximum (as taught by both Chakravorty et al and Hiddessen et al), would be a simple substitution of one set of known elements for another set of known elements with predictable results.
Claim(s) 1-4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chakravorty et al (2017) as cited on the IDS of 02/24/2026 including the Supplementary Information in view of Hiddessen et al (US PG Pub 2018/0147573) as applied to claims 10-13 above, and further in view of Romanov et al (US Pat 10,239,909; March 26, 2019).
Chakravorty et al in view of Hiddessen et al renders obvious methods comprising detection target nucleic acids using a 5’-nuclease real-time PCR method and LSS dyes (including Pulsar 650) and SSS dyes with similar adsorption peak maxima and different emission peak maxima, and teach that the use of dyes with similar adsorption peak maxima and different emission peak maxima expands the utility of the multiplex assays by separating detection of dyes with similar adsorption peak maxima by detecting their emission at different wavelengths.
Chakravorty et al in view of Hiddessen et al does not teach the use of dyes with similar emission peak maxima and different absorption peak maxima.
However, Chakravorty et al does provide a table demonstration that various dyes have similar emission peak maxima and different absorption peak maxima (e.g.: CF4, CF8 and CF9 in Fig. 1A). And the use of dyes with similar emission and different absorption was known in the prior art and is taught by Romanov et al.
Romanov et al teaches (e.g.: col. 14) the detection of nucleic acids which are labeled with dyes where the emission bands for the dyes are overlapping such that emission in the overlap region of the spectrum causes both labels to emit fluorescence at the same detection wavelength, and the detection if effected when each dye is only excited by one of the excitation wavelengths, and thus the dyes are separately detectable due to their distinct excitation profiles. When the excitation for the dyes occur in different regions of the spectrum, the presence of a dye can be determined by optically distinguishing the excitation.
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have used dyes with different absorption maxima and similar emission maxima, as taught by Romanov et al and as taught by Chakravorty et al in the methods rendered obvious by Chakravorty et al in view of Hiddessen et al. The us of different dye pair would have been the simple substitution of one known element for another predictable results. The skilled artisan would have been further motivated to modify the methods of Chakravorty et al in view of Hiddessen et al with the teachings of Romanov et al based on the expressed teachings of Romanov et al (e.g.: col. 15) that using dyes with different absorption maxima and similar emission maxima allows the use of instrumentation with a single emission channel, which may therefore reduce or avoid the need for multiple emission filters, where the detection system may have a single detection channel set to a fixed emission wavelength.
Claim(s) 4 and 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chakravorty et al (2017) as cited on the IDS of 02/24/2026 including the Supplementary Information in view of Hiddessen et al (US PG Pub 2018/0147573) and Romanov et al (US Pat 10,239,909; March 26, 2019), as applied to claims 1-4 above, and further in view of Mueller et al (US PG Pub 2017/0002398.
Chakravorty et al in view of Hiddessen et al and Romanov et al renders obvious methods comprising detection target nucleic acids using a 5’-nuclease real-time PCR method and LSS and SSS dyes with similar emission peak maxima and different absorption peak maxima.
Chakravorty et al in view of Hiddessen et al and Romanov et al does not teach the particular dye that is Chromeo 494, as recited in claims 4 and 5.
However, the use of Chromeo 494 as label for nucleic acids, and the absorption and emission peak maxima of Chromeo 494 were known in the prior art and are taught by Mueller et al (e.g.: p.6 – Claim 7; p.5 – Table 1).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have used the dye Chrome 494 in the methods rendered obvious by Chakravorty et al in view of Hiddessen et al and Romanov et al. Where the prior art teaches the absorption and emission maxima of Chromeo 494, and teaches that the dye is suitable for use in real-time PCR methods, the use of Chromeo 494 and pairing it with a dye that has a similar emission maximum and different absorption maximum (as taught by Romanov et al), would be a simple substitution of one set of known elements for another set of known elements with predictable results.
Conclusion
No clam is allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Eastwood et al (US Pat 7,919,325) teaches the analysis of dyes with similar emission spectra but different excitation spectra (e.g.: col. 15)..
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683
Prosecution Insights