Dynamics of nucleic acids on and around carbon nano-materials and in the presence of excess salt:
The hybrids of single-walled carbon nanotube (SWCNT) and single stranded DNA (ssDNA) are novel nanoscale materials having remarkable applications in nanotechnology. The ab- sorption 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 pi-pi stacking between the DNA bases and the sp hybridized carbon atoms of the carbon nan- otube. 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. Current investigation involves monitoring salt-induced aggregation dynamics of nucleic acids using all atom simulations.
Relevant Publications:
1. Salt Induced Structural Collapse, Swelling and Signature of Aggregation of Two ssDNA Strands: Insights from Molecular Dynamics Simulation - Soham Sarkar, Atanu Maity, Aditya Sarma Phukon, Soumadwip Ghosh and Rajarshi Chakrabarti, J. Phys. Chem. B 123, 47 (2019).
2. Unzipping of Double-Stranded Ribonucleic Acids by Graphene and Single-Walled Carbon Nanotube: Helix Geometry versus Surface Curvature - Soumadwip Ghosh and Rajarshi Chakrabarti, J. Phys. Chem. C 120, 22681 (2016).
3. Spontaneous unzipping of Xylonucleic acid on Single-walled carbon nanotube: a computational study - Soumadwip Ghosh and Rajarshi Chakrabarti, J. Phys. Chem. B 120, 3642 (2016).
4. Probing the salt concentration dependent nucleobase distributions in a single stranded DNA-single walled nanotube hybrid with molecular dynamics - Soumadwip Ghosh, Nisheet Patel and Rajarshi Chakrabarti, J. Phys. Chem. B 120, 455 (2016).