Conformational Changes of Single-Stranded Hairpin DNA Covalently Immobilized on Solid Surfaces Investigated by Molecular Dynamics Simulations

Abstract

Molecular beacons (MBs) are stem-loop hairpin structured nucleic acid probes that have shown greater sensitivity and specificity over linear DNA probes. For high-throughput DNA detection, MBs are often covalently immobilized on a variety of solid surfaces (e.g., glass slides and gold surfaces). The performance of immobilized MBs on solid surfaces has been found to be dependent on the stability and orientation of their stem-loop structures on surfaces. At present, however, there is still a lack of high-resolution experimental characterization approaches for determining the conformational behaviors of immobilized MBs on surfaces. Herein, we investigated the structure and dynamics of immobilized MB probe in NaCl and MgCl2 solutions respectively by performing all-atom molecular dynamics simulations. We found that the single immobilized MB probe maintained a stable stemloop structure in the MgCl2 solution, while it undergone significant structural distortion in the NaCl solution. The results show that Mg2+ ions have a stronger stabilizing effect on immobilized hairpins compared with Na+ ions, which is attributed to their greater shielding ability for the negatively charged phosphate backbone. Moreover, the hydrogen-bonding dynamics in the hairpin's loop and stem parts were analyzed respectively to further understand the effect of the base–base interactions on conformational stability of MBs immobilized on solid surfaces. The findings in this work help to optimize the design of MBs biosensors, thus further improving their performance of nucleic acid detection.