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 .
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has been timely paid, the finality of the previous Office action has been withdrawn pursuant to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 02/24/2026 has been entered.
Receipt is acknowledged of an amendment, filed on 02/24/2026, in which claims 26-28 were amended, claims 1-7, 10-25, 29 and 30 were canceled, claims 8 and 9 were previously presented and claims 31-52 were newly added. Claims 27 and 28 are currently withdrawn due to an election/restriction requirement in a previous office action.
Claims 8, 9, 26 and 31-52 are currently under examination.
Priority
Acknowledgment is made of applicant' s claim for priority based on a provisional application filed as 62/832,171 on 04/10/2019.
All claims are given the priority date of 04/10/2019.
Response to Amendment - Claim Objections
The previous objection to claim 8 has been withdrawn as indicated in the previous advisory action due to the amendments filed on 02/24/2026.
Response to Amendments - Claim Rejections - 35 USC § 112
The previous rejection of claims 1, 2, 4-26 and 30 has been withdrawn in view of Applicant’s amendments/cancellation of the claims filed on 02/24/2026.
Response to Arguments - Claim Rejections - 35 USC § 102
The previous rejection of claims 1, 4 and 26 under 35 U.S.C. 102(a)(2) as being unpatentable by Afonin et al (WO 2017/139758 A1) has been withdrawn in view of Applicant’s amendments to the claims filed on 02/24/2026.
The previous rejection of claims 1, 2, 4-7 10-21, 23 and 25-26 under 35 U.S.C. 102(a)(2) as being unpatentable by Shapiro et al (WO 2013/075132 A1) has been withdrawn in view of Applicant’s amendments to the claims filed on 02/24/2026.
Claim Rejections - 35 USC § 103
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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.
Claims 8, 9, 26 and 31-52 are rejected under 35 U.S.C. 103 as being unpatentable by Afonin et al (Nucleic Acids Research, Volume 42, Issue 3, 1 February 2014, Pages 2085–2097) in view of Santangelo et al (Nucleic Acids Research, 2004, Vol. 32, No. 6 e57; Pgs. 1-9; Supplemental Material Pages 1/22-22-22) and Shapiro et al (WO 2013/075132 A1; Cited in previous office action) as evidenced by O’Leary et al (Cancer Res 2018;78(13 Suppl): Abstract nr 5104). This is a NEW Rejection.
Regarding claim 8, Afonin teaches a DNA/RNA hybrid nucleic acid nanoparticle comprising:(a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA and/or RNA; and(b) at least one single stranded RNA output strand, wherein no portion of the at least one trigger toehold hybridizes to any portion of the at least one output strand, the at least one trigger toehold is complementary and hybridizes to a first target sequence when the DNA/RNA hybrid nucleic acid nanoparticle is in the presence of the first target sequence, further wherein the DNA/RNA hybrid nucleic acid nanoparticle comprises a sense construct and an antisense construct, wherein the sense construct and the antisense construct are not connected to each other, and wherein the at least one output strand separates from the DNA/RNA hybrid nucleic acid nanoparticle when the at least one trigger toehold hybridizes to the first target sequence, wherein the sense construct comprises a first trigger toehold and a first output strand, the antisense construct comprises a second trigger toehold and a second output strand, and the first trigger toehold and wherein the sense construct comprises a first DNA strand comprising a sequence that is complementary to the first output strand and the antisense construct comprises a second DNA strand comprising a sequence that is complementary to the second output strand, wherein the first DNA strand is connected to the first trigger toehold and the second DNA strand is connected to the second trigger toehold (Page 2086, Figure 1).
Afonin does not teach the DNA/RNA hybrid nucleic acid nanoparticle does not contain target sequence and where the target sequence is in a target RNA.
Shapiro teaches hybrid nucleic acid nanoparticle comprising single stranded sense and antisense strand where the sense strand has a sequence complementary to the antisense strand and the antisense strand is complementary of the target RNA in order to hybridize with the target RNA (Page 13, Lines 2-12; Page 17, Paragraphs | and 2). Shapiro teaches the therapeutic RNA switch, or tswRNA, is an RNA molecule or RNA containing molecular complex that has at least one region that is complementary to a trigger sequence such as the recognition domain (toehold in the instant claims) that can be either RNA or DNA (Page 12, Lines 26-29). Shapiro teaches upon binding to the trigger sequence, the tswRNA goes through a conformational change that allows the dicer to cleave and release the strand (Page 13, Lines 9-12). Shapiro teaches that the structure is a small hairpin RNA where it is a single stranded RNA that has self-duplexed (Page 43, Lines 18-19). Shapiro teaches the use of the nucleotide sequence encoding CTGF as a therapeutic strand (Page 5 bridging Page 6). Shapiro teaches a region of the CTGF mRNA acts as trigger (the gene CTGF is highly expressed in a variety of cancers; CTGF is also known under the synonyms CCN2 or IGFBP8) (Page 56, Lines 23-25). Shapiro teaches CTGF will trigger the active conformation of the RNA switch, leading to the formation of an siRNA targeting the anti-apoptotic gene Survivin (Page 54, Lines 28-29).
Shapiro does not teach the first trigger toehold and the second trigger toehold are complementary to adjacent positions within the first target sequence.
Santangelo teaches 2'-deoxy-oligonucleotide probes designed to detect mRNA, featuring a stem-loop structure with a fluorophore at the 5' end and a quencher at the 3' end, utilizing a Dual FRET (Förster Resonance Energy Transfer) mechanism to minimize false positives (Page 1, Column 1 bridging Column 2). Santangelo teaches that the dual FRET molecular beacons showed a significant increased detection of the mRNA KRAS target sequence as compared to the single molecular beacons (Page 4, Column 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin to include the first trigger toehold and the second trigger toehold are complementary to adjacent positions within the first target sequence as taught by Shapiro and Santangelo because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand, Santangelo teaches increased biostability and detection using dual molecular beacon probes for targeting adjacently to a KRAS mRNA target site as compared to the single molecular beacons and Shapiro teaches the use of the DNA/RNA hybrid switches in order to modulate expression levels of other genes, such as CTGF, for the purpose of treatment and the gene CTGF is highly expressed in a variety of cancers.
One would have been motivated to make such a modification in order to receive the expected benefit of specificity in the treatment of CTGF related treatments such as inhibition leading to reduction in downstream expression leading to treatment of tumor formation and/or growth as taught by Shapiro as well as increased biostability and detection of the mRNA KRAS target sequence as taught by Santangelo.
Regarding claim 9, Afonin teaches the DNA sense construct trigger toehold is within 10 nucleotide bases from the sequence complimentary to the Malachite Green sequence (denoted mg1; is directly next to the DNA sense trigger toehold in the sequence denoted DNA for H1 (mg1_s_s)) which can be considered the first output sequence as well as the DNA antisense construct trigger toehold is within 10 nucleotide bases from the sequence complimentary to the Malachite Green sequence (denoted mg2; directly next to the DNA sense trigger toehold in the sequence denoted DNA for H1 (mg2_a_a)) which could be considered the second output strand (Page 2086, Figure 1; Supplemental Page 2, Malachite green (MG) aptamer split in two RNA strands and Page 4, Hybrids designed to release MG aptamer and two siRNAs). Afonin teaches the DNA toeholds capable of interacting with each other are 100% complementary to each other as shown in the supplemental information (Supplemental Page 4; sequences denoted DNA for H1 and DNA for H2 under Hybrids designed to release MG aptamer and two siRNAs).
Regarding claim 26, Afonin teaches that the nanoparticle is a therapeutic pharmaceutical composition (Page 2085, Abstract and Page 2095, Column 2).
Regarding claims 31 and 32, Afonin does not teach wherein the first target sequence is part of a naturally occurring mRNA.
Santangelo teaches that the dual FRET molecular beacons showed a significant increased detection of the mRNA KRAS target sequence as compared to the single molecular beacons (Page 4, Column 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin to include the first trigger toehold and the second trigger toehold are complementary to adjacent positions within the first target sequence as taught by Santangelo because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand and Santangelo teaches increased biostability and detection using dual molecular beacon probes for targeting adjacently to a KRAS mRNA target site as compared to the single molecular beacons.
One would have been motivated to make such a modification in order to receive the expected benefit of increased biostability and detection of the mRNA KRAS target sequence as taught by Santangelo.
Regarding claim 33, Afonin teaches the output strands were not were modified at the 2’ nucleotides (Page 2086, Figure 1 and Supplemental information Page 4; sequences denoted DNA for H1 and DNA for H2 under Hybrids designed to release MG aptamer and two siRNAs).
Regarding claim 34, Afonin does not teach wherein the first target sequence comprises a portion of nucleotides encoding KRAS.
Santangelo teaches that the dual FRET molecular beacons showed a significant increased detection of the mRNA KRAS target sequence as compared to the single molecular beacons (Page 4, Column 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin to include the first trigger toehold and the second trigger toehold are complementary to adjacent positions within the first target sequence as taught by Santangelo because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand and Santangelo teaches increased biostability and detection using dual molecular beacon probes for targeting adjacently to a KRAS mRNA target site as compared to the single molecular beacons.
One would have been motivated to make such a modification in order to receive the expected benefit of increased biostability and detection of the mRNA KRAS target sequence as taught by Santangelo.
Regarding claim 35, Afonin and Santangelo do not teach the use of CTGF as the target for modulation of expression.
Shapiro teaches the use of RNA switches comprising several adjacent regions that can bind to a trigger sequence as well as sense and antisense sequences that can form an siRNA-like structure (Page 2, Lines 1-11). Shapiro teaches the use of the nucleotide sequence encoding CTGF as a therapeutic strand (Page 5 bridging Page 6). Shapiro teaches a region of the CTGF mRNA acts as trigger (the gene CTGF is highly expressed in a variety of cancers; CTGF is also known under the synonyms CCN2 or IGFBP8) (Page 56, Lines 23-25). Shapiro teaches CTGF will trigger the active conformation of the RNA switch, leading to the formation of an siRNA targeting the anti-apoptotic gene Survivin (Page 54, Lines 28-29).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin and Santangelo to include the modulation of expression of CTGF as taught by Shapiro because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand, Santangelo teaches increased biostability and detection using dual molecular beacon probes for targeting adjacently to a KRAS mRNA target site as compared to the single molecular beacons and Shapiro teaches the use of the DNA/RNA hybrid switches in order to modulate expression levels of other genes, such as CTGF, for the purpose of treatment and the gene CTGF is highly expressed in a variety of cancers.
One would have been motivated to make such a modification in order to receive the expected benefit of specificity in the treatment of CTGF related treatments such as inhibition leading to reduction in downstream expression leading to treatment of tumor formation and/or growth as taught by Shapiro.
Regarding claim 36, Afonin teaches wherein the first trigger toehold and the second trigger toehold hybridize to each other than the first output strand hybridizes to the second output strand and forms a double stranded output strand that separates from the nanoparticle
Afonin does not teach wherein the first trigger toehold and the second trigger toehold hybridize to adjacent positions within the first target sequence.
Santangelo teaches 2'-deoxy-oligonucleotide probes designed to detect mRNA, featuring a stem-loop structure with a fluorophore at the 5' end and a quencher at the 3' end, utilizing a Dual FRET (Förster Resonance Energy Transfer) mechanism to minimize false positives (Page 1, Column 1 bridging Column 2). Santangelo teaches that the dual FRET molecular beacons showed a significant increased detection of the mRNA KRAS target sequence as compared to the single molecular beacons (Page 4, Column 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin to include the first trigger toehold and the second trigger toehold are complementary to adjacent positions within the first target sequence as taught by Santangelo because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand and Santangelo teaches increased biostability and detection using dual molecular beacon probes for targeting adjacently to a KRAS mRNA target site as compared to the single molecular beacons.
One would have been motivated to make such a modification in order to receive the expected benefit of increased biostability and detection of the mRNA KRAS target sequence as taught by Santangelo.
Regarding claims 37 and 38, Afonin teaches the entire length of the hybrid sequences designed to release a MG aptamer and two siRNA strands (which would then hybridize to each other creating a double stranded siRNA structure) are 83 nucleic acids long (Supplemental material Page 4, Hybrids designed to release MG aptamer and two siRNAs). Therefore, the first DNA strand of the sense construct comprises from about 1 to about 100 nucleic bases between the first trigger toehold and the sequence that is complementary to the first output strand and the second DNA strand of the antisense construct comprises from about 1 to about 100 nucleic bases between the second trigger toehold and the sequence that is complementary to the second output strand.
Regarding claims 39-44, Afonin does not teach that the DNA/RNA hybrid comprises a hairpin loop and further wherein the hairpin loop comprises from about 12 to about 20 base pairs.
Santangelo teaches the sequences of the donor molecular beacon and acceptor molecular beacon where the stem sequence is underlined and the loop sequence comprises 16 to 17 nucleic acids in length (Page 2, Table 1). Santangelo teaches the hairpin structure also acts as an adjustable energy penalty for beacon opening which improves probe specificity (Page 1, Column 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin to include the hairpin loop structures as taught by Santangelo because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand and Santangelo teaches the hairpin structure also acts as an adjustable energy penalty for beacon opening which improves probe specificity.
One would have been motivated to make such a modification in order to receive the expected benefit of the hairpin structure also acts as an adjustable energy penalty for beacon opening which improves probe specificity as taught by Santangelo.
Regarding claim 45-47, Afonin teaches that when the first trigger toehold hybridizes to the second trigger toehold, the first output strand and second output strand are released and capable of hybridizing together (Page 2086, Figure 1).
Afonin does not teach wherein when the first trigger toehold hybridizes to the first target sequence, the hairpin loop is disrupted and wherein when the second trigger toehold hybridizes to the first target sequence, the hairpin loop is disrupted.
Santangelo teaches the donor molecular beacon and acceptor molecular beacon are both a hairpin loop structure and when introduced to the target binding site, hairpin loops are disrupted and the DNA sequences bind adjacently to each other on the mRNA target sequence (Page 2, Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin to include the hairpin loop structures as taught by Santangelo because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand and Santangelo teaches the hairpin structure also acts as an adjustable energy penalty for beacon opening which improves probe specificity.
One would have been motivated to make such a modification in order to receive the expected benefit of the hairpin structure also acts as an adjustable energy penalty for beacon opening which improves probe specificity as taught by Santangelo.
Regarding claims 48-50, Afonin teaches that the double stranded RNA output is an siRNA (Page 2086, Figure 1).
Regarding claim 51, Afonin teaches the DNA/RNA hybrid switch system for use in treating breast cancer.
Afonin does not teach the specific target sequence and biomarkers associated with that target sequence.
Santangelo teaches a region of the KRAS mRNA target sequence for DNA dual FRET molecular beacons to bind to the KRAS gene sequence (Page 2, Column 1 bridging column 2 and Table 1). O’Leary is cited only as evidence to show that KRAS is highly expressed in a variety of cancers, specifically in breast cancer with known biomarkers including prolactin (Page 1, Abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Afonin to include the first trigger toehold and the second trigger toehold are complementary to adjacent positions within the first target sequence as taught by Santangelo because Afonin teaches it is within the ordinary skill in the art to use a RNA/DNA hybrid complex that comprising (a) at least one trigger toehold, wherein the at least one trigger toehold comprises DNA; and (b) at least one single stranded RNA output strand and Santangelo teaches increased biostability and detection using dual molecular beacon probes for targeting adjacently to a KRAS mRNA target site as compared to the single molecular beacons.
One would have been motivated to make such a modification in order to receive the expected benefit of increased biostability and detection of the mRNA KRAS target sequence as taught by Santangelo.
Regarding claim 52, Afonin teaches that no strands of the nanoparticle were modified at the 2’ nucleotides (Page 2086, Figure 1 and Supplementary information pages 2-5).
Response to Arguments - Claim Rejections - 35 USC § 103
The previous rejection of claims 22 and 24 under 35 U.S.C. 103 as being unpatentable by Shapiro et al (WO 2013/075132 A1) in view of Brown (US 9,809,819 B2) has been withdrawn in view of Applicant’s cancellation of the claims filed 02/24/2026.
Conclusion
No claims are allowed.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637