Equilibrium and Transport Distributions of a DNA Dodecamer in Hydrophilic Nanopores

Abstract

Abstract Selective and controlled delivery of genetic cargo to a living cell, using encapsulation into nanoporous solids, involves a three-step kinetics: i) confinement of the biomolecule, followed by ii) diffusion along the endohedral volume, and finallly iii) ejection of the biological material towards the cellular interior. In order to study the thermodynamical and kinetical properties associated with the process, we employ atomically detailed computer experiments to probe the encapsulation of double-stranded canonical B-DNA, (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), into electrically charged (hydrophilic) carbon nanotubes with diameters in the range D = 3 – 4 nm. For that purpose, Classical Molecular Dynamics simulations are run coupled with Hamiltonian-biasing algorithms to probe the systems’ free-energy landscapes and independently determine the relevant kinetic distributions. It is observed that nucleic acid encapsulation is thermodynamically spontaneous (∼ 40 kJ/mol), and translation within the confining solids is anisotropic only for the largest topology (D = 4 nm), with the nucleic acid exhibiting Fickian self-diffusion coefficients in the range Deff = 0.537 – 0.954 × 10–9 m2/s. Occurring in the early stages subsequent to confinement (t > 2 ns), a previously unobserved dynamical transition from a Fickian (∝ t) to a single-file regime (∝ t1/2) is interpreted in terms of exclusion volumes and electrostatic interactions betweem the NaCl buffer and DNA. Physiological conditions employed throughout (310 K, [NaCl] = 134 mM) allow the extrapolation of results to in vivo systems, constituting a landmark for nucleic acid encapsulation in the context of cellular delivery and personalized therapeutics