DNA Hairpin Adsorption on Gold Surfaces: Temperature and Salt Concentration Effects on Structure

© 2020 CSIRO. The structure and dynamics of a DNA hairpin is investigated for its potential use in molecular sensing, as well as the suitability of the DNA hairpin as a possible temperature-sensitive actuating nano-spacing agent. At present, little is known regarding the molecular-scale details of the structural change of DNA aptamers in response to an external stimulus such as heat, when adsorbed to sensor-relevant substrates such as gold or graphene. An in-depth understanding at the atomistic level is required to probe the transition of aptamers from an ordered state to a disordered state when adsorbed on a surface, but is challenging to obtain from experiments alone. Molecular simulation offers a complementary approach. Here we use molecular dynamics simulations of an exemplar DNA hairpin in aqueous solution and adsorbed onto Au(111), at a range of temperatures and salt concentrations. Our findings provide new insights into the structural changes that occur and predict the conformational preferences that are likely to be present in an experimental system.