Nanoscopic Characterization of DNA within Hydrophobic   Pores:Thermodynamics and Kinetics
  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. 
Fernando J.A.L. Cruz and Juan J. de Pablo and Jos\'e P.B. Mota
physics.bio-ph cond-mat.mes-hall physics.chem-ph