[gmx-users] Unwrapping of ssDNA

[soumadwip ghosh]

Hi all,
        I am a little bit confused about the unwrapping dynamics of a
single stranded nucleic acid from the surface of a carbon nanotube. Say I
have a NA-CNT hybrid and I think in presence of excess salt the adsorbed
DNA will adopt a partially collapsed state thus breaking the initial
contacts with the CNT atoms. If this task is to be achieved do you think
that the concentration of added salt should be high enough or one can try
it at the physiological conc (150mM) of NaCl. I performed the simulation at
this concentration but no unwrapping was observed. Is there any possibility
of the said unwrapping if the salt concentration is raised from the
perspective of my understanding or I am going terribly wrong somewhere? I
would be grateful to any sort of discussion in this regard.

Thanking you,
Soumadwip Ghosh
Senior Research Fellow
IITB
Mumbai
India