Effect of handle length and microsphere size on transition kinetics in single-molecule experiments

When subject to constant tension, a DNA or RNA hairpin will typically make abrupt transitions between the open and closed state. Although the transition kinetics are an intrinsic property of the molecule, the transition rates measured in single-molecule experiments can be influenced by the configuration of the measurement system. We investigate the transition kinetics for a DNA hairpin held under constant force by an optical trap as a function of microsphere size and double-stranded DNA handle length. We find the apparent transition lifetime cannot be expressed as a function of the drag coefficient of the microsphere alone or as a function of time scales relevant to the optical trap. The apparent transition lifetime is found to be a linear function of the factor β(eff)·α(handle), where β(eff) is the effective drag coefficient of the microsphere near the surface and α(handle) is the stiffness of the DNA tether. The results provide insight into the perturbation to the hairpin transition kinetics due to experimental configuration and guidance for designing single-molecule experiments which determine the intrinsic molecular kinetics.