Rupture of DNA aptamer: new insights from simulations

Mishra, Rakesh Kumar ; Nath, Shesh ; Kumar, Sanjay (2015) Rupture of DNA aptamer: new insights from simulations Journal of Chemical Physics, 143 (16). Article ID 164902. ISSN 0021-9606

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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 and adenosinetriphosphate, 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.

Item Type:Article
Source:Copyright of this article belongs to AIP Publishing.
Keywords:DNA; Entropy; Hydrogen Bonding; Fluorescence Spectroscopy; Protein Ligand Interactions
ID Code:102641
Deposited On:02 Feb 2018 04:23
Last Modified:02 Feb 2018 04:23

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