title: Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form.
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 ~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.
authors.affiliation: Requimte/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal.
authors.forename: Fernando J A L
authors.initials: FJ
authors.lastname: Cruz
authors.affiliation: Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Juan J
authors.initials: JJ
authors.lastname: de Pablo
authors.affiliation: Requimte/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal.
authors.forename: José P B
authors.initials: JP
authors.lastname: Mota
mesh_terms: D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D058608:Nanopores / Q000648:ultrastructure; D037742:Nanotubes, Carbon / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D037742:Nanotubes, Carbon; D004247:DNA