title: Rupture of DNA aptamer: New insights from simulations.
abstract: 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.
authors.affiliation: Department of Physics, Banaras Hindu University, Varanasi 221 005, India.
authors.forename: Rakesh Kumar
authors.initials: RK
authors.lastname: Mishra
authors.affiliation: Department of Physics, Banaras Hindu University, Varanasi 221 005, India.
authors.forename: Shesh
authors.initials: S
authors.lastname: Nath
authors.affiliation: Department of Physics, Banaras Hindu University, Varanasi 221 005, India.
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kumar
mesh_terms: D000249:Adenosine Monophosphate / Q000737:chemistry*; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001665:Binding Sites; D019277:Entropy; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013050:Spectrometry, Fluorescence
chemical_list: D052157:Aptamers, Nucleotide; D000249:Adenosine Monophosphate