The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition

Methods: Five different simulations have been conducted by varying starting structures and temperatures.

Background: Aptamers are RNA/DNA biomolecules representing an emerging class of protein interactors and regulators. Despite the growing interest in these molecules, current understanding of chemical-physical basis of their target recognition is limited. Recently, the characterization of the aptamer targeting the protein-S8 has suggested that flexibility plays important functional roles. We investigated the structural versatility of the S8-aptamer by molecular dynamics simulations.