Modeling coupled dynamics using DNA hairpin

Abstract

Secondary or tertiary structures of protein or RNA often undergo structural equilibrium. Often, structural dynamics of one domain influences to other domain’s structural equilibrium. These coupling is known to be a key feature in regulation of protein or RNA folding, and providing allosteric property, especially in intrinsically disordered protein. Despite the importance and universality of this effect, this coupled dynamics has been poorly understood because of complexity of the system. In this research, we suggest DNA hairpin as a model system for coupled dynamics. We constructed 86 bp ssDNAs with hairpin structure at the 5' end. Single base in stem and loop are labeled with Cy5 and Cy3 respectively, in order to observe conformational state using Förster resonance energy transfer(FRET). Short (9 nucleotides) or long (25 nucleotides) ssDNA fragment which is complementary to the downstream of hairpin stem was incubated together to induce perturbation to the hairpin forming equilibrium. Conformation change of each single hairpin was recorded by single molecule FRET experiment. We successfully reproduced change in hairpin dynamics when only the ssDNA binding equilibrium is dynamic. Our findings suggest simple and reductive model system of coupled dynamics using DNA hairpin.