Molecular dynamics study of thrombin capture by aptamers TBA26 and TBA29 coupled to a DNA origami

The fabrication of DNA origamis is one of the very few possibilities to create nanostructures with precise atomistic-tailored geometries in a variety of shapes. In addition, these origamis can be functionalized or be impregnated with specialised aptamers in order to convert them into nanosensors or to tune them with pre-specified properties simply by impregnating single-stranded DNA or RNA chains (aptamers) via the precise features of DNA pairing. We performed molecular dynamics simulations to determine the relative energetics associated with the capture of thrombin by two aptamers TBA26 and TBA29 attached to a rectangular DNA origami. The molecular simulations provided detailed structural information of aptamer-enzyme interactions which are crucial for the efficient design of aptamer-based biosensors. In addition, the simulations showed a remarkable selectivity of the biosensor assembly for thrombin. The detection, capture, and sensing of enzymes is of great significance in biomedicine. In particular, the detection of thrombin is a major task in cardiovascular diagnostics and therapeutics. On the other hand, our simulations can be extended to detect biotoxins or any other chemical or biological agent by simply choosing proper aptamers. Finally, the problems due to the large number of atoms involved as well as the quality of the approximations are also discussed.