US 12,077,807 B2
Compositions and methods for analyte detection using nanoswitches
Arun Richard Chandrasekaran, Albany, NY (US); Clinton H. Hansen, Cambridge, MA (US); Mounir Ahmad Koussa, Somerville, MA (US); Kenneth Anders Halvorsen, Glenmont, NY (US); and Wesley Philip Wong, Cambridge, MA (US)
Assigned to The Research Foundation for The State University of New York, Albany, NY (US); and Children's Medical Center Corporation, Boston, MA (US)
Appl. No. 15/738,982
Filed by The Research Foundation for The State University of New York, Albany, NY (US); and Children's Medical Center Corporation, Boston, MA (US)
PCT Filed Jun. 27, 2016, PCT No. PCT/US2016/039654
§ 371(c)(1), (2) Date Dec. 21, 2017,
PCT Pub. No. WO2017/003950, PCT Pub. Date Jan. 5, 2017.
Claims priority of provisional application 62/185,582, filed on Jun. 27, 2015.
Prior Publication US 2018/0223344 A1, Aug. 9, 2018
Int. Cl. C12Q 1/6816 (2018.01); C12Q 1/6818 (2018.01); C12Q 1/6839 (2018.01); G01N 27/447 (2006.01); G01N 30/86 (2006.01); G01N 30/02 (2006.01)
CPC C12Q 1/6816 (2013.01) [C12Q 1/6818 (2013.01); C12Q 1/6839 (2013.01); G01N 27/447 (2013.01); G01N 30/8675 (2013.01); G01N 2030/027 (2013.01)] 9 Claims
 
1. 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.