We report on an experiment and calculations that determine the thermal motion of a voltageclamped 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 DNA's 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.

We report on an experiment and calculations that determine the thermal motion of a voltage-clamped single-stranded DNA-NeutrAvidin complex in a Mycobacterium smegmatis porin A nanopore. The electric force and diffusion constant of DNA inside a Mycobacterium smegmatis porin A pore were determined to evaluate the thermal position fluctuations of DNA. 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 how a reduction in thermal position fluctuations can be achieved by increasing the electrophoretic force used in nanopore sequencing devices.

We report effective charges and diffusion constants of several different single-stranded DNA oligonucleotides trapped in an MspA nanopore. Nucleotide identity is found to have a substantial influence on effective charges and diffusion constants. These quantities are determined from escape time experiments for a DNA molecule attached to a NeutrAvidin molecule that, unlike the DNA, does not pass through the pore. Correlations are reported between oligonucleotide effective charges and current blockages, and between their diffusion constants and DNA-induced current blockage fluctuations. We also report an unanticipated source of current fluctuations that reflects a discrete blockage current level structure. We posit that this is associated with interactions between the NeutrAvidin molecule and the MspA nanopore.