Toehold-Mediated Displacement of an Adenosine-Binding Aptamer from a DNA Duplex by its Ligand.
DNA is increasingly used to engineer dynamic nanoscale circuits, structures, and motors, many of which rely on DNA strand-displacement reactions. The use of functional DNA sequences (e.g., aptamers, which bind to a wide range of ligands) in these reactions would potentially confer responsiveness on such devices, and integrate DNA computation with highly varied molecular stimuli. By using high-throughput single-molecule FRET methods, we compared the kinetics of a putative aptamer-ligand and aptamer-complement strand-displacement reaction. We found that the ligands actively disrupted the DNA duplex in the presence of a DNA toehold in a similar manner to complementary DNA, with kinetic details specific to the aptamer structure, thus suggesting that the DNA strand-displacement concept can be extended to functional DNA-ligand systems.
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, 80309, USA.
Jon H
0000-0002-1752-2783
JH
Monserud
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, 80309, USA.
Katherine M
KM
Macri
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, 80309, USA. daniel.schwartz@colorado.edu.
Daniel K
DK
Schwartz
D000241:Adenosine / Q000737:chemistry*; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D057166:High-Throughput Screening Assays; D008024:Ligands
D052157:Aptamers, Nucleotide; D008024:Ligands; D004247:DNA; D000241:Adenosine
DNA; FRET; aptamers; single-molecule microscopy; strand displacement