Thermal motion of DNA in an MspA pore

Abstract

We report on an experiment and calculations that determine the thermal motion of a voltage-clamped ssDNA-NeutrAvidin complex in an MspA nanopore. The electric force and diffusion constant of DNA inside an MspA pore have been determined in order to evaluate DNAs thermal position fluctuations. We show that an out-of-equilibrium state returns to equilibrium so quickly that experiments usually measure a weighted average over the equilibrium position distribution. Averaging over the equilibrium position distribution is consistent with results of state-of-the-art nanopore sequencing experiments. It is shown that a reduction in thermal averaging can be achieved by increasing the electrophoretic force used in nanopore sequencing devices.