Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form
| Autor: | Juan J. de Pablo, José P. B. Mota, Fernando J. A. L. Cruz |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
FOS: Physical sciences
General Physics and Astronomy Carbon nanotube law.invention chemistry.chemical_compound Nanopores law Physics - Chemical Physics Mesoscale and Nanoscale Physics (cond-mat.mes-hall) Nanobiotechnology A-DNA Physics - Biological Physics Physical and Theoretical Chemistry Chemical Physics (physics.chem-ph) chemistry.chemical_classification Condensed Matter - Mesoscale and Nanoscale Physics Hydrogen bond Nanotubes Carbon Biomolecule Biomolecules (q-bio.BM) Hydrogen Bonding DNA Nanopore Crystallography Dodecameric protein chemistry Quantitative Biology - Biomolecules Biological Physics (physics.bio-ph) FOS: Biological sciences Thermodynamics |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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