Force spectroscopy of the thrombin-aptamer interaction: Comparison between AFM experiments and molecular dynamics simulations

Abstract

Previous literature on dynamic force spectroscopy of the thrombin-aptamer complex has shown significantly different force magnitudes even at similar AFM tip velocities, implying the need for a more elaborate evaluation of the force interaction. In this study, we employ a combination of experimental and computational methods to reveal comprehensively how the unbinding force can possibly depend on the loading rate, coverage density, binding rate, linker stiffness and binding buffer composition. In addition, we utilize enhanced analytical techniques that include autocorrelation function, probability density convolution, and Poisson distribution to determine the dissociation force quanta of multiple bond dissociation from force spectroscopy experiments. We then predict the unbinding force measured in the experiments by using atomistic simulation data with significantly broader loading rate range following a continuum model. The dissociation forces of thrombin-aptamer complex are found to be lower than forces associated with the breakdown of G-quadruplex on aptamer, while comparable to forces associated with DNA melting, which indicates the complex dissociation could be more likely attributed to the bond breakage between thrombin and aptamer, rather than the collapse of G-quadruplex on aptamer.