Nanoscopic Characterization of DNA within Hydrophobic Pores:Thermodynamics and Kinetics

Abstract

The energetic and transport properties of a double-stranded DNA dodecamer encapsulated in hydrophobic carbon nanotubes are probed employing two limiting nanotube diameters, D=4 nm and D=3 nm, corresponding to (51,0) and (40,0) zig-zag topologies, respectively. It is observed that the thermodynamically spontaneous encapsulation in the 4 nm nanopore (40 kJ/mol) is annihilated when the solid diameter narrows down to 3 nm, and that the confined DNA termini directly contact the hydrophobic walls with no solvent slab in-between. During the initial moments after confinement (2-3 ns),the biomolecule translocates along the nano pore's inner volume according to Fick's law (t) with a self-diffusion coefficient D=1.713 x 10-9m2/s, after which molecular diffusion assumes a single-file type mechanism (t1/2). As expected, diffusion is anisotropic, with the pore main axis as the preferred direction, but an in-depth analysis shows that the instantaneous velocity probabilities are essentially identical along the x, y and z directions. The 3D velocity histogram shows a maximum probability located at v=30.8 m/s, twice the observed velocity for a single-stranded three nucleotide DNA encapsulated in comparable armchair geometries (v=16.7 m/s, D=1.36-1.89 nm). Because precise physiological conditions (310 K, [NaCl] = 134 mM) are employed throughout, the present study establishes a landmark for the development of next generation in vivo drug delivery technologies based on carbon nanotubes as encapsulation agents.