Mishra Rakesh Kumar, Nath Shesh, Kumar Sanjay
Department of Physics, Banaras Hindu University, Varanasi 221 005, India.
J Chem Phys. 2015 Oct 28;143(16):164902. doi: 10.1063/1.4933948.
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.
双链DNA中的碱基口袋（非互补碱基对）在生物过程中起着至关重要的作用。由于热涨落，它会降低DNA的稳定性，而在DNA适体的情况下，小分子，例如单磷酸腺苷和三磷酸腺苷，会与被称为“结合口袋”的碱基口袋形成额外的氢键，从而增强稳定性。我们通过对DNA粗粒化模型进行朗之万动力学模拟，随后进行原子模拟，研究了碱基口袋和结合口袋对DNA适体稳定性的影响。这里报道了温度和力引起的分离存在显著差异，这需要通过单分子实验进一步研究。
