Nanoscopic Characterization of DNA within Hydrophobic Pores:Thermodynamics and Kinetics

TL;DR

This study investigates the thermodynamics and kinetics of double-stranded DNA encapsulation in hydrophobic carbon nanotubes, revealing size-dependent stability, diffusion behavior, and velocity profiles relevant for drug delivery applications.

Contribution

It provides detailed insights into DNA behavior within hydrophobic nanotubes, including thermodynamic stability and diffusion mechanisms, under physiological conditions.

Findings

Spontaneous encapsulation occurs in 4 nm nanotubes but not in 3 nm.

DNA translocates via Fick's law initially, then single-file diffusion.

Velocity distribution peaks at 30.8 m/s, higher than in single-stranded DNA.

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.