title: 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 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.
authors.affiliation: Department of Physics, Harvard University, Cambridge, Massachusetts.
authors.forename: Bo
authors.initials: B
authors.lastname: Lu
authors.affiliation: Department of Physics, Harvard University, Cambridge, Massachusetts.
authors.forename: Stephen
authors.initials: S
authors.lastname: Fleming
authors.affiliation: School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts.
authors.forename: Tamas
authors.initials: T
authors.lastname: Szalay
authors.affiliation: Department of Physics, Harvard University, Cambridge, Massachusetts; School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts. Electronic address: golovchenko@physics.harvard.edu.
authors.forename: Jene
authors.initials: J
authors.lastname: Golovchenko
mesh_terms: D001360:Avidin / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004058:Diffusion; D008957:Models, Genetic; D008958:Models, Molecular; D009038:Motion; D020102:Mycobacterium smegmatis; D058608:Nanopores; D018408:Patch-Clamp Techniques; D018272:Porins / Q000378:metabolism*; D013696:Temperature
chemical_list: D004277:DNA, Single-Stranded; D018272:Porins; C121838:mspA protein, Mycobacterium smegmatis; C093483:neutravidin; D001360:Avidin