Conformational Thermodynamics of DNA Strands in Hydrophilic Nanopores

Enhanced sampling techniques spanning a submicrosecond time scale reveal that a double-stranded DNA dodecamer can be spontaneously encapsulated into (51, 0) and (40, 0) single-walled carbon nanotubes under the influence of an electric field, leading to hybrids with a 40 kJ/mol enhanced free energy. The confinement mechanism allows the nucleic acid to retain its mobility, diffusing anisotropically along the endohedral volume, visiting regions of space determined by entropic factors (diameter, free volume) and linked by a thermodynamical highway. In spite of the energetic similarities between both topologies (4.1 x 10(3) kJ/mol), the biomolecule favors positioning either parallel to the nanopore central axis (40, 0) or in close contact with the solid walls (51, 0), encasing a hollow cylindrical domain of diameter 1-1.5 nm in the latter. Precise physiological conditions allow the extrapolation of results to in vivo systems and constitute a novel and thorough contribution to nanotube technology in the areas of nucleic acid encapsulation/delivery and personalized therapeutics.