Nucleic acid detection methods

Patent metadata

Field	Value
Publication number	US-2026092313-A1
Application number	US-202519294190-A
Country	US
Kind code	A1
Filing date	Aug 7, 2025
Priority date	Aug 7, 2024
Publication date	Apr 2, 2026
Grant date	—

Abstract

The disclosure relates to methods and systems for the detection of low-quantity (e.g., 1×102 copies/μL) target nucleic acids (e.g., genomic RNA and/or genomic DNA).

First claim

1 . A method of detecting a target nucleic acid in a sample comprising:
(i) contacting a sample in a reaction mixture with
(a) a capture oligonucleotide that is immobilized to a surface via a silane-containing perfluorinated linker, wherein the capture oligonucleotide comprises a capture domain that is complementary to a first region of the target nucleic acid, and
(b) a sense oligonucleotide that is functionalized with a first member of a binding pair and comprises a target-binding domain that is complementary to a second region of the target nucleic acid, wherein the first region of the target nucleic acid does not overlap with the second region of the target nucleic acid, and
(ii) optionally removing nucleic acids that are not bound to the capture oligonucleotide from the reaction mixture, (iii) adding a detectable molecule that is conjugated to a second member of the binding pair to the reaction mixture, and (iv) detecting signal from surface-bound detectable label, wherein surface-bound signal at a level above background noise is indicative of the presence of the target nucleic acid in the sample.

2 . A method of determining the concentration of a target nucleic acid in a sample, the method comprising:
(i) contacting a sample comprising the target nucleic acid with a sense oligonucleotide and a capture oligonucleotide that is immobilized to a surface via a silane-containing perfluorinated linker to produce a surface-immobilized target nucleic acid, wherein the capture oligonucleotide comprises a capture domain that is complementary to a first region of the target nucleic acid, wherein the sense oligonucleotide is functionalized with a first member of a binding pair and comprises a target-binding domain that is complementary to a second region of the target nucleic acid, and wherein the first region of the target nucleic acid does not overlap with the second region of the target nucleic acid; (ii) contacting the surface-immobilized target nucleic acid with a detectable molecule that is conjugated to a second member of the binding pair; and (iii) determining the concentration of the target nucleic acid based on detection of the detectable molecule.

3 . The method of claim 1 , wherein the target nucleic acid is a ribonucleic acid (RNA).

4 . The method of claim 1 , wherein the capture domain and/or the target-binding domain comprises one or more locked nucleotides (LNAs).

5 . The method of claim 1 , wherein the silane-containing perfluorinated linker comprises the structure of Formula (I):

6 . The method of claim 1 , wherein the surface is a glass surface.

7 . The method of claim 1 , wherein the detectable molecule is a fluorescent molecule.

8 . The method of claim 7 , wherein the fluorescent molecule is a fluorophore or a quantum dot.

9 . The method of claim 1 , wherein the first member of the binding pair is biotin and/or the second member of the binding pair is streptavidin.

10 . A system for detecting a target nucleic acid in a sample, the system comprising:
a substrate configured to receive a sample such that the sample is contacted in a reaction mixture with
(a) a capture oligonucleotide that is immobilized to a surface on the substrate via a silane-containing perfluorinated linker, wherein the capture oligonucleotide comprises a capture domain that is complementary to a first region of the target nucleic acid, and
(b) a sense oligonucleotide that is functionalized with a first member of a binding pair and comprises a target-binding domain that is complementary to a second region of the target nucleic acid, wherein the first region of the target nucleic acid does not overlap with the second region of the target nucleic acid,
the substrate further configured to receive a detectable molecule that is conjugated to a second member of the binding pair such that the detectable molecule is added to the reaction mixture, and a detector configured to detect signal from surface-bound detectable label, wherein surface-bound signal at a level above background noise is indicative of the presence of the target nucleic acid in the sample.

11 . The system of claim 10 , wherein the detector comprises an image sensor.

12 . The system of claim 10 , further comprising:
a removal component configured to remove nucleic acids that are not bound to the capture oligonucleotide from the reaction mixture.

13 . A system for determining the concentration of a target nucleic acid in a sample, the system comprising:
a substrate configured to receive the sample comprising the target nucleic acid such that the sample is contacted with a sense oligonucleotide and a capture oligonucleotide that is immobilized to a surface on the substrate via a silane-containing perfluorinated linker to produce a surface-immobilized target nucleic acid, wherein the capture oligonucleotide comprises a capture domain that is complementary to a first region of the target nucleic acid, wherein the sense oligonucleotide is functionalized with a first member of a binding pair and comprises a target-binding domain that is complementary to a second region of the target nucleic acid, and wherein the first region of the target nucleic acid does not overlap with the second region of the target nucleic acid, the substrate further configured to receive a detectable molecule that is conjugated to a second member of the binding pair such that the surface-immobilized target nucleic acid is contacted with the detectable molecule; and a processor configured to determine the concentration of the target nucleic acid based on detection of the detectable molecule.

14 . The system of claim 10 , wherein the target nucleic acid is a ribonucleic acid (RNA).

15 . The system of claim 10 , wherein the capture domain and/or the target-binding domain comprises one or more locked nucleotides (LNAs).

16 . The system of claim 10 , wherein the silane-containing perfluorinated linker comprises the structure of Formula (I):

17 . The system of claim 10 , wherein the surface is a glass surface.

18 . The system of claim 10 , wherein the detectable molecule is a fluorescent molecule.

19 . The system of claim 18 , wherein the fluorescent molecule is a fluorophore or a quantum dot.

20 . The system of claim 10 , wherein the first member of the binding pair is biotin and/or the second member of the binding pair is streptavidin.

Assignees

• Charles Stark Draper Laboratory Inc

Inventors

• Moran Isaac
• Kelly Kim
• Turo Mike
• Rosenberger Erin

Classifications

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• C12Q1/6834

  Enzymatic or biochemical coupling of nucleic acids to a solid phase · CPC title

• C12Q1/6825 Primary

  Nucleic acid detection involving sensors · CPC title