Dynamics of B-DNA in Electrically Charged Solid Nanopores

5 years ago

Dynamics of B-DNA in Electrically Charged Solid Nanopores

José P. B. Mota, Fernando J. A. L. Cruz

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 (∝ t) only during a short initial time-window (2 ns), being followed by an apparent transition to a single-file regime (∝ 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 ≈ 27 m/s. The short time Fickian self-diffusivities determined, D_eff = 0.537 × 10^–9 to 0.954 × 10^–9 m²/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.

Publisher URL: http://dx.doi.org/10.1021/acs.jpcc.7b03167

DOI: 10.1021/acs.jpcc.7b03167