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

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({sup *}CP{sup *}GP{sup *}CP{sup *}GP{sup *}AP{sup *}AP{sup *}TP{sup *}TP{sup *}CP{sup *}GP{sup *}CP{sup *}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 ∼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 asmore » encapsulation media for next generation drug delivery technologies.« less
Authors:
 [1] ;  [2] ;  [3] ;  [2] ;  [1]
  1. Requimte/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516 (Portugal)
  2. (United States)
  3. Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)
Publication Date:
OSTI Identifier:
22420089
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 140; Journal Issue: 22; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICAL METHODS AND COMPUTING; APPROXIMATIONS; BONDING; CARBON NANOTUBES; DNA; ENCAPSULATION; FREE ENERGY; STABILITY