Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form

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Abstract

Although carbon nanotubes are potential candidates for DNA encapsulation and subsequent delivery of biological payloads to living cells, the thermodynamical spontaneity of DNA encapsulation under physiological conditions is still a matter of debate. Using enhanced sampling techniques, we show for the first time that, given a sufficiently large carbon nanotube, the confinement of a double-stranded DNA segment, 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', is thermodynamically favourable under physiological environments (134 mM, 310 K, 1 bar), leading to DNA-nanotube hybrids with lower free energy than the unconfined biomolecule. A diameter threshold of 3 nm is established below which encapsulation is inhibited. The confined DNA segment maintains its translational mobility and exhibits the main geometrical features of the canonical B form. To accommodate itself within the nanopore, the DNA's end-to-end length increases from 3.85 nm up to approximately 4.1 nm, due to a similar to 0.3 nm elastic expansion of the strand termini. The canonical Watson-Crick H-bond network is essentially conserved throughout encapsulation, showing that the contact between the DNA segment and the hydrophobic carbon walls results in minor rearrangements of the nucleotides H-bonding. The results obtained here are paramount to the usage of carbon nanotubes as encapsulation media for next generation drug delivery technologies. (C) 2014 AIP Publishing LLC.

Original languageEnglish
Article number225103
Number of pages10
JournalJournal of Chemical Physics
Volume140
Issue number22
DOIs
Publication statusPublished - 14 Jun 2014

Keywords

  • PARTICLE MESH EWALD
  • MOLECULAR-DYNAMICS
  • STRANDED-DNA
  • NUCLEIC-ACID
  • SIMULATION
  • ADSORPTION
  • DISTRIBUTIONS
  • FIELD

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