Stacking interactions involving non-Watson–Crick basepairs: dispersion corrected density functional theory studies

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发布日期 2017-10-06
DOI 10.1039/C7CP04904H
影响因子 3.676
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摘要

The G:A basepair, stabilized by hydrogen bonding through the sugar edge of guanine and Hoogsteen edge of adenine in trans orientation (G:A S:HT), appears very frequently in the solved RNA structures and is very stable. We have carried out stacking energy analyses of two sequences, namely C:G W:WC::G:A S:HT and G:C W:WC::G:A S:HT (‘:’ represents basepairing and ‘::’ represents stacking interactions), formed by this non-Watson–Crick basepair, by DFT-D. We have scanned nearly the complete phase space by modeling structures of these sequences using different values of the basepair orientation parameters to determine the most stable conformations. It is found that the most stable conformations are rather far from the most frequently found orientations. We have considered the effect of sugar–phosphate backbone connectivity as an energy penalty arising from deformation of pseudo bond lengths between C1′ atoms of successive bases along the strands. Augmentation of stacking energy from DFT-D by this coarse grain energy gives predicted structures extremely similar to the experimentally determined ones. It has been observed that the best stacking with small twist values is associated with positive roll and negative slide values, which are similar to their values in A-RNA structures for most sequences. Among the two base pair steps, C:G W:WC::G:A S:HT appears to be more stable in terms of stacking energy as compared to G:C W:WC::G:A S:HT possibly due to larger stacking overlap in the former one.

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来源期刊

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
自引率: 10.3%
年发文量: 3036

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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