Dynamics of B-DNA in Electrically Charged Solid Nanopores

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Abstract

Delivery of genetic cargo to a cell via nanopore encapsulation relies on the assumption that subsequent to confinement, the biological load can diffuse along the endohedral volume to reach the desired exit point. Probing the corresponding kinetics is therefore of fundamental importance for nanopore-based technology to achieve cellular delivery. Atomically detailed computer experiments are used to probe the dynamics of canonical B-DNA double strands (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') encapsulated into electrically charged carbon nanotubes (D = 3-4 nm) under physiological conditions; nucleic acid translation obeys Fick's law (proportional to t) only during a short initial time-window (2 ns), being followed by an apparent transition to a single-file regime (proportional to t(1/2)) in which DNA exhibits preferential diffusion paths. The nucleic acid disfavors positioning at the nanopore termini, and while in the D = 4 nm tube DNA diffuses anisotropically, in the smaller diameter solid the preferred mode of translation is a self-rotation about the double-helix axis. This anisotropicity is attributed to free-volume, for instantaneous velocities are identical, < v >(max) approximate to 27 m/s. The short time Fickian self-diffusivities determined, D-eff = 0.537 X 10(-9) to 0.954 X 10(-9) m(2)/s, reveal for the first time that electrostatic attraction between the walls and DNA induces a slowing down of molecular diffusion in hydrophilic nanotubes as compared to pristine topologies.
Original languageEnglish
Pages (from-to)16568-16575
JournalJournal of Physical Chemistry C
Volume121
Issue number30
DOIs
Publication statusPublished - 2017

Keywords

  • PARTICLE MESH EWALD
  • CARBON NANOTUBES
  • MOLECULAR-DYNAMICS
  • STRANDED-DNA
  • TRANSPORT
  • THERMODYNAMICS

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