  Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a
crucial role in biological processes. Because of thermal fluctuations, it can
lower the stability of DNA, whereas, in case of DNA aptamer, small molecules
e.g. adenosinemonophosphate(AMP), adenosinetriphosphate(ATP) etc, form
additional hydrogen bonds with base-pockets termed as "binding-pockets", which
enhance the stability. Using the Langevin Dynamics simulations of coarse
grained model of DNA followed by atomistic simulations, we investigated the
influence of base-pocket and binding-pocket on the stability of DNA aptamer.
Striking differences have been reported here for the separation induced by
temperature and force, which require further investigation by single molecule
experiments.
