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 examiner handling this application has changed. The new examiner on this case is Kailey Cash (kailey.cash@uspto.gov) in AU1683. Any correspondence relating to the instant application should be directed to this examiner.
This Office Action is in reply to Applicants’ correspondence of 1/30/2026. Applicants’ remarks and amendments have been fully and carefully considered but are not found to be sufficient to put this application in condition for allowance. New grounds of rejection are presented in this Office Action. Any rejections or objections not reiterated herein have been withdrawn in light of the amendments to the claims or as discussed in this Office Action. This Action is NON-FINAL.
Claim Status
Claims 1-2, 4-18, 53, and 72 are pending and being examined on the merits.
Specification
Applicant’s amendment to the specification to properly denote trade names or marks used in commerce is acknowledged. The objection to the specification is withdrawn in light of these amendments.
Claim Objections
The objection to claims 1 and 53 are withdrawn in light of Applicant’s amendments to the claims.
Claim Rejections - 35 USC § 112d – Failure to Further Limit
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 4 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 4, which depends from claim 1, recites the limitation “wherein the terminator hairpin of the non-extensible oligonucleotide is unable to hybridize to the upstream sequence of the DNA template”. However, claim 1 already describes that the terminator hairpin is not the reverse complement of the upstream sequence of the DNA template, indicating that it cannot hybridize to the upstream sequence of the template. Therefore, claim 4 does not further limit claim 1. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
Withdrawn: The 102 and 103 claim rejections, as presented in the Office Action of 9/2/2025, are withdrawn. New claim rejections are presented below. Given the presentation of new claim rejections, this action is non-final.
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.
Claims 1-2, 4-9, 13-14, 53, and 72 are rejected under 35 U.S.C. 103 as being unpatentable over Singh (Singh et al., Molecular Biology 2000) in view of Zhang 2015 (Zhang et al., WO 2015/179339 A1).
Claim 1: Singh teaches a composition comprising a DNA template, a DNA polymerase, and an oligonucleotide primer. Singh teaches that the DNA template comprises an upstream sequence and a probe binding sequence. Singh teaches that the oligonucleotide primer comprises, from 5’ to 3’, a binding sequence that is at least 70% identical to the reverse complement of the probe binding sequence of the DNA template, and a terminator hairpin positioned at the 3’ end of the oligonucleotide that comprises a first stem sequence, a second stem sequence that is the reverse complement of the first stem sequence, and a first sloop sequence positioned between the first and second stem sequences (Table 1, Primer 1). The oligonucleotide of Singh does not comprise an artificial chemical modification or a non-natural DNA nucleotide at its 3’ end (Table 1, Primer 1).
Singh does not teach that the terminator hairpin of the oligonucleotide is not the reverse complement of the upstream sequence of the DNA template. The oligonucleotide primer of Singh comprises a terminator hairpin that is the reverse complement of the upstream sequence of the DNA template (Experimental Procedures – Target Sequence Generation). Singh demonstrates that the formation of a secondary structure 3’ terminal hairpin alone is enough to inhibit amplification efficiency of a PCR that uses this terminal hairpin structure as a forward primer (Figure 2). However, the inability of polymerases to extend off of a non-complementary 3’ terminal end of a primer is known in the art, as taught by Zhang 2015.
Zhang 2015 teaches an oligonucleotide primer that is non-homologous at the 3’ end, which prevents enzymatic extension by a polymerase (paragraph [058, 101]).
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 composition of Singh with the non-complementary sequence aspect of Zhang 2015. One would be motivated to do so given the teachings by Zhang 2015 that having oligonucleotides that prevent enzymatic extension are desirable for creating blocking sequences for the selective amplification of rare target mutations (paragraph [009-010]). Zhang 2015 also teaches that providing blocker oligonucleotides without complex backbone or nucleotide modifications is desirable given that that makes the reagents more inexpensive (paragraph [017]). Singh teaches that some level of amplification may still occur given the ability of the hairpin structure to dissolve and anneal to the template and provide a substrate for extension. The substitution of a non-complementary sequence that does not base pair with the upstream template sequence provides the predictable result of additional inhibition of amplification by the hairpin structure at the 3’ end.
Singh in view of Zhang 2015 do not explicitly teach that this structure cannot be enzymatically extended by a high-fidelity DNA polymerase with 3’ to 5’ exonuclease activity. However, the combination of Singh and Zhang teaches all aspects of the terminator hairpin structure which is non-extensible, as claimed by the current composition. Therefore, the structure as taught by Singh in view of Zhang 2015 is inherently non-extensible by a high-fidelity DNA polymerase with 3’ to 5’ exonuclease activity, absent any additional limitations that are particularly needed for said blockage.
Claim 2: Singh teaches that the binding sequence of the non-extensible oligonucleotide is 10 nucleotides long (Table 1, Primer 1).
Claim 4: Zhang 2015 teaches that the sequence that prevents enzymatic extension is unable to hybridize to the upstream sequence of the DNA template (paragraph [058, 101] and Figure 8).
Claim 5-6: Singh teaches that the first stem sequence is 4 nucleotides long (Table 1, Primer 1).
Claim 7-8: Singh teaches that the second stem sequence is 4 nucleotides long (Table 1, Primer 1).
Claim 9: Singh teaches that the first and second stem sequence are both 4 nucleotides long (Table 1, Primer 1).
Claim 13-14: Singh teaches that the first loop sequence is 4 nucleotides long (Table 1, Primer 1).
Claim 53: Singh in view of Zhang 2015 teach the composition of claim 1, as described above. Zhang teaches inclusion of a tail sequence at the very end of the oligonucleotide composition that is not complementary to the upstream sequence of the DNA template (reads on at most 40% identical to the reverse complement of the upstream sequence of the DNA template; see Figure 8).
Claim 72: Singh in view of Zhang 2015 teach the composition of claim 1, as described above. Zhang teaches a method of selectively inhibiting a PCR amplification of a template DNA having a selected sequence for the specific amplification of rare variants (Abstract). Singh in view of Zhang teach use of a forward primer, reverse primer, and dNTPs in combination with a non-extensible oligonucleotide under conditions suitable for DNA polymerase activity and subjecting the mixture to at least 7 rounds of thermocycling wherein the template DNA possibly comprises the target DNA template and possibly comprises a background DNA template molecule (paragraph [069-073, 079] of Zhang 2015).
Claims 10-11 are rejected under 35 U.S.C. 103 as being unpatentable over Singh (Singh et al., Molecular Biology 2000) in view of Zhang 2015 (Zhang et al., WO 2015/179339 A1) as applied to claims 1-2, 4-9, 13-14, 53, and 72 above, and further in view of Lamoureux (Lamoureux et al 2006; cited on PTO-892 of 9/2/2025) and Zhang 2012 (Zhang et al., WO 2012/058488 A1; cited on PTO-892 of 9/2/2025).
The teachings of Singh in view of Zhang 2015 with regard to claim 1 are detailed above.
Singh in view of Zhang 2015 do not teach that the DNA hairpin stem sequence is 5’-TCTC-3’ and 5’-GAGA-3’.
Claim 10-11: Lamoureux teaches a DNA hairpin with complementary stem loop sequences of four nucleotides in length (e.g., Lamoureux et al., title; page 85, right column, para 1). Zhang 2012 teaches a DNA hairpin with stem complementary sequences of 5’-TCTC-3’ and 5’-GAGA-3’ (e.g., Zhang Fig 6).
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 used the hairpin with stem complementary sequences of 5’-TCTC-3’ and 5’-GAGA-3’ of Zhang 2012 with the composition of Singh in view of Zhang 2015. The skilled artisan would have been motivated to use the hairpin sequences of Zhang 2012 with the composition of Singh in view of Zhang 2015 by the teachings of Lamoureux, that varying the stem sequences altered physical characteristics, bond strength and stem and hairpin structure (e.g., Lamoureux et al., page 91, table 4; page 90, right column, first para) and by the teachings of Singh that different stem lengths alter melting temperature and other characteristics of the hairpin and stem (e.g., Singh, Table 1) and a skilled artisan would understand that optimizing oligonucleotide length and sequence would lead to desired specific characteristics (i.e., melting temperature, bond strength etc.). Further Zhang 2012 teaches that melting temperatures vary from target to target (e.g., Zhang 2012 page 2, para 3) and that their hairpin primers are designed to bind with high specificity to only intended targets and provide a high degree of specificity even in high nucleic acid background systems (e.g., Zhan page 3, para 1). Thus, the addition of the hairpin sequences of Lamoureux and Zhang 2012 to the composition of Singh in view of Zhang 2015 would have been a simple combination of known methods to yield predictable results.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Singh (Singh et al., Molecular Biology 2000) in view of Zhang 2015 (Zhang et al., WO 2015/179339 A1) as applied to claims 1-2, 4-9, 13-14, 53, and 72 above, and further in view of Lamoureux (Lamoureux et al 2006; cited on PTO-892 of 9/2/2025).
The teachings of Singh in view of Zhang 2015 with regard to claim 1 are detailed above.
Singh in view of Zhang 2015 do not teach that the DNA hairpin stem sequence is 5’- GTTC-GAAC-3’.
Claim 12: Lamoureux teaches a DNA hairpin with complementary stem loop sequences of four nucleotides in length (i.e., 5’- GTTC-GAAC-3’) (e.g., Lamoureux et al., title; page 85, right column, para 1).
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 used the well-known hairpin stem 5’- GTTC-GAAC-3’, of Lamoureux with the non-extensible oligonucleotide with hairpin and stem of Singh in view of Zhang 2015. The skilled artisan would have been motivated to use the hairpin stem sequences of Lamoureux, because different stem sequences affect the melting temperature, structure, and bond strength of the hairpin itself, and as such, can be tailored to match the thermal requirements of the nucleic acid (e.g., Lamoureux, page 91, table 4; page 90, right column, first para). Thus, the addition hairpin stem of Lamoureux to the non-extensible oligonucleotide hairpin of Singh in view of Zhang 2015 would have been a simple combination of known methods to yield predicable results and a skilled artisan would know to tailor their nucleic acid reagents to the needs of their protocol.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Singh (Singh et al., Molecular Biology 2000) in view of Zhang 2015 (Zhang et al., WO 2015/179339 A1) as applied to claims 1-2, 4-9, 13-14, 53, and 72 above, and further in view of Khutsishvili (Khutsishvili et al., 2020; cited on PTO-892 of 9/2/2025).
The teachings of Singh in view of Zhang 2015 with regard to claim 1 are detailed above.
Singh in view of Zhang 2015 do not teach that the DNA loop sequence is 5’-GCAA-3’.
Claim 15: Khutsishvili teaches a hairpin loop of 4 nucleotides and having the sequence GCAA (e.g., Khutsishvili et al., title; page 66a, left column, para 1).
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 used the loop sequence of Khutsishvili with the non-extensible oligonucleotide with hairpin and stem of Singh in view of Zhang 2015. The skilled artisan would have been motivated to use the loop sequence of Khutsishvili because different loop sequences affect the melting temperature, structure, and bond strength of the hairpin, and as such, can be tailored to match the thermal requirements of the nucleic acid protocol and by the teachings of Khutsishvili that their experimentation of altering the hairpin loop sequence impacted the thermal stability of the structure, and that GCAA yielded generally higher melting temperatures, but the overall stability of the hairpin and stem structure were affected by the loop sequence, as well as the stem sequence it was paired with (e.g., Khutsishvili, page 66a, right column, para 1). Thus, the addition hairpin loop of Khutsishvili et al to the non-extensible oligonucleotide hairpin of Singh in view of Zhang 2015 would have been a simple combination of known methods to yield predicable results and a skilled artisan would know to tailor their nucleic acid reagents to the needs of their protocol.
Claims 16 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Singh (Singh et al., Molecular Biology 2000) in view of Zhang 2015 (Zhang et al., WO 2015/179339 A1) as applied to claims 1-2, 4-9, 13-14, 53, and 72 above, and further in view of Smolke (US Patent 8,772,464 B2; cited on PTO-892 of 9/2/2025).
The teachings of Singh in view of Zhang 2015 with regard to claim 1 are detailed above.
Singh in view of Zhang 2015 do not teach that the oligonucleotide comprises a second hairpin between the binding sequence and the terminal hairpin, but these were known in the art and were taught by Smolke (US Patent 8772464, patented 8 July 2014).
Claim 16: Smolke teaches an oligonucleotide comprising two hairpin structures, with a terminal hairpin and a middle hairpin that is between the terminal hair pin and the binding sequence, where each hairpin has complementary stem sequences (e.g., Smolke Fig. 8A), reading on the limitations “oligonucleotide further comprises a middle hairpin positioned between the binding sequence and the terminator hairpin, the middle hairpin comprising: a third stem sequence, a fourth stem sequence, wherein the fourth stem sequence is the reverse complement of the third stem sequence, and a second loop sequence positioned between the third stem sequence and the fourth stem sequence” of the instantly rejected claim 16.
It would have been prima facie obvious before the effective filing date of the claimed invention for a person having ordinary skill in the art to have used the multiple hairpin oligonucleotide of Smolke with the composition of Singh in view of Zhang 2015. The skilled artisan would have been motivated to use the multiple hairpin oligonucleotide of Smolke based on the teachings of Smolke that their invention can be designed for use in hybridization-dependent detection assays and are useful for detecting the presence, absence or amount of an analyte (e.g., Smolke column 2, lines 26-30). Thus, the addition of the dual-hairpin oligonucleotide of Smolke to the composition of Singh in view of Zhang 2015 would have been a simple combination of known methods to yield predicable results.
Claim 18: Singh teaches that the first and second stem sequence are both 4 nucleotides long in the terminator hairpin (Table 1, Primer 1).
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Singh (Singh et al., Molecular Biology 2000) in view of Zhang 2015 (Zhang et al., WO 2015/179339 A1) and Smolke (US Patent 8,772,464 B2; cited on PTO-892 of 9/2/2025), as applied to claims 1-2, 4-9, 13-14, 16, 18, 53, and 72 above, and further in view of Lamoureux (Lamoureux et al., 2006; cited on PTO-892 of 9/2/2025).
The teachings of Singh in view of Zhang 2015 and Smolke with regard to claims 1 and 16 are detailed above.
Singh in view of Zhang 2015 and Smolke do not teach that the 3’ most nucleotide in the terminator hairpin is a cytosine.
Claim 17: Lamoureux teaches a DNA hairpin with complementary stem loop sequences of four nucleotides in length and a 3’ terminal cytosine (e.g., Lamoureux, title; page 85, right column, para 1).
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 used the hairpin with the 3’ terminal cytosine of Lamoureux with the composition of Singh in view of Zhang 2015. The skilled artisan would have been motivated to use the hairpin sequences of Lamoureux with the composition of Singh in view of Zhang 2015 given the assertion of Lamoureux that varying the stem sequences altered physical characteristics, bond strength and stem and hairpin structure (e.g., Lamoureux, page 91, table 4; page 90, right column, first para) and by the teachings of Singh that different stem lengths alter melting temperature and other characteristics of the hairpin and stem (e.g., Singh, Table 1) and a skilled artisan would understand that optimizing oligonucleotide length and sequence would lead to desired specific characteristics (i.e., melting temperature, bond strength etc.). Thus, the addition of the 3’ terminal cytosine in the hairpin to the composition of Singh in view of Zhang 2015 would have been a simple combination of known methods to yield predictable results.
Response to Remarks
Applicant’s arguments, see pages 7-9 of Remarks, filed 1/30/2026, with respect to the rejection(s) of claim(s) 1-5, 7, 53, and 72 under 35 USC 102 have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Singh and Zhang 2015 (see above). These new grounds of rejection presented in this Office Action make this action non-final.
Conclusion
No claims are allowed.
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
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