title: Probing the Salt Concentration Dependent Nucelobase Distribution in a Single-Stranded DNA-Single-Walled Carbon Nanotube Hybrid with Molecular Dynamics.
abstract: The hybrids of single-walled carbon nanotube (SWCNT) and single stranded DNA (ssDNA) are novel nanoscale materials having remarkable applications in nanotechnology. The absorption of nucleobases on the surface of a SWCNT depends strongly on the ionic strength of the medium. In this paper, using atomistic molecular dynamics we have shown that at low salt concentration ssDNA wraps on the surface of SWCNT through hydrophobic π-π stacking between the DNA bases and the sp(2)-hybridized carbon atoms of the carbon nanotube. At high salt concentration, however, the DNA molecule adopts a partially folded structure and the ssDNA-SWCNT wrapping gets weakened significantly due to the self-stacking of the DNA bases. Our study can find relevance in CNT mediated gene delivery processes where subsequent unwrapping of the gene from its carrier is anticipated across the cell membrane regulated by an existing salt concentration gradient.
authors.affiliation: Department of Chemistry, Indian Institute of Technology , Powai, Mumbai, 40076, India.
authors.forename: Soumadwip
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Department of Chemistry, Indian Institute of Technology , Powai, Mumbai, 40076, India.
authors.forename: Nisheet
authors.initials: N
authors.lastname: Patel
authors.affiliation: Department of Chemistry, Indian Institute of Technology , Powai, Mumbai, 40076, India.
authors.forename: Rajarshi
authors.initials: R
authors.lastname: Chakrabarti
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D015335:Molecular Probes; D037742:Nanotubes, Carbon; D009696:Nucleic Acids / Q000737:chemistry*; D012492:Salts / Q000032:analysis*
chemical_list: D004277:DNA, Single-Stranded; D015335:Molecular Probes; D037742:Nanotubes, Carbon; D009696:Nucleic Acids; D012492:Salts