Compositions and methods for analyte detection using nanoswitches
AssigneesThe Research Foundation for The State University of New York, Children's Medical Center Corporation
InventorsArun Richard Chandrasekaran, Clinton H. Hansen, Mounir Ahmad Koussa, Kenneth Anders Halvorsen, Wesley Philip Wong
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Abstract
Provided herein are nucleic acid-based nanoswitches that can detect specific nucleic acids and other analytes types by for example a simple gel electrophoresis readout. Binding of the target to the nanoswitches induces a conformation change from a linear, open conformation to a looped, closed conformation. These nanoswitches may be used in diagnostic assays such as nucleic acid-based diagnostic assays, to detect, measure and/or purify a variety of targets including low abundance targets.
Claims9
A method for stabilizing a nanoswitch in a looped conformation, comprising
- providing a nucleic acid-based nanoswitch, conjugated to a first binding partner and a second binding partner, wherein the first binding partner is bound (i) directly to the second binding partner or (ii) to an analyte bound to the second binding partner, in a first binding interaction, and the nanoswitch thereby adopts a looped conformation, and
- contacting the nucleic acid-based nanoswitch in the looped conformation with a latch nucleic acid to form a second binding interaction in the nanoswitch, thereby stabilizing the nanoswitch in the looped conformation without affecting loop size,
- wherein the nucleic acid-based nanoswitch comprises a scaffold nucleic acid hybridized to a plurality of oligonucleotides, wherein the plurality of oligonucleotides comprises a first oligonucleotide conjugated to the first binding partner, a second oligonucleotide conjugated to the second binding partner, a third oligonucleotide partially hybridized to the scaffold nucleic acid and comprising a 3′ overhang, a fourth oligonucleotide partially hybridized to the scaffold nucleic acid and comprising a 5′ overhang that is not complementary to the 3′ overhang, wherein the 3′ and 5′ overhangs each comprise at least 7 nucleotides that are fully complementary to the latch nucleic acid,
- wherein the second binding interaction (a) comprises the latch nucleic acid hybridized to the 3′ overhang of the third oligonucleotide and the 5′ overhang of the fourth oligonucleotide and (b) occurs as a result of the first binding interaction, and
- wherein the latch nucleic acid does not directly hybridize to the scaffold nucleic acid.
Dependencies are inferred from the claim text.