# Nanoscopic Characterization of DNA within Hydrophobic Pores:Thermodynamics and Kinetics

Source: [Nanoscopic Characterization of DNA within Hydrophobic Pores:Thermodynamics and Kinetics](<https://www.sota2.com/research/paper/68fa33621e209131ce88fb3a>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-24T20:02:45.256Z

Authors: Fernando J.A.L. Cruz, Juan J. de Pablo, Jos\\'e P.B. Mota

Published: 2016-05-04T18:12:13.000Z

## 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.

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1605.01366>)

[PDF](<https://arxiv.org/pdf/1605.01366.pdf>)