Single Molecule Study of the Role of Aptamer Secondary Structure in the Dynamics of Aptamer-Ligand Binding Interactions

Nucleic acid aptamers are a rapidly expanding technology due to a high affinity for their target molecules, stability, low cost of production, and ease of chemical modification. Aptamers can be engineering to bind to a wide range of molecules, which results in a sequence that has high affinity for the target ligand after several rounds of selection. These aptamers adopt a number of secondary structures when the ligand is bound, including stem/loops bulges, g-quadruplexes, hairpins, and psuedoknots; yet, little is understood about the mechanism by which the aptamer-ligand binding occurs. For a number of aptamers, an adaptive recognition model of binding has been proposed, where the aptamer adopts an unfolded conformation in solution and folds upon addition of the target molecule. However, some aptamers appear to have a prefolded structure, as they undergo little to no conformational change upon target addition. We employed single molecule Forster resonance energy transfer (FRET) to measure hybridization dynamics between an aptamer and a complementary “capture” strand immobilized on a fused silica surface. We found that the ligand disrupts the DNA duplex when a toehold is present, similar to DNA strand displacement reactions. This suggests that the mechanics of DNA strand displacement can be extended to improve the understanding and development of functional aptamer-ligand systems such as biosensors, molecular motors, and biocomputational circuits.