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Journal of Molecular Modeling

, Volume 15, Issue 6, pp 615–622 | Cite as

How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex?

Original Paper

Abstract

This study reports on ab initio calculations of adenine - cytosine complexes in two different context alignments appearing in B-DNA. The influence of adenine modification by hydroxyl radical on the stability of the complexes is also discussed. The analysis was performed on over 40 crystallographic structures for each of the sequence contexts. In most cases, modification of adenine by hydroxyl radical leads to less negative intermolecular interaction energies. The issue of the influence of alteration of structural base step parameters on the stability of modified and unmodified adenine - cytosine complexes is also addressed. Analysis of the dependence of intermolecular interaction energy on base step parameters reveals that for twist and shift modification of adenine by hydroxyl radical leads to quite different interaction energy profiles in comparison with unmodified complexes. In order to elucidate the physical origins of this phenomenon, i.e. to analyze how the modification of adenine by hydroxyl radical is reflected in the change of intermolecular interaction energy components, a variational-perturbational decomposition scheme was applied at the MP2/aug-cc-pVDZ level of theory.

Keywords

Intermolecular interactions Nucleic acid base complexes Stacking interactions 

Notes

Acknowledgements

This work was supported by computational grants from WCSS (Wroclaw Centre for Networking and Supercomputing) and Poznan Supercomputing and Networking Center (PCSS). The allocation of computing time is greatly appreciated.

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Faculty of Pharmacy, Collegium MedicumNicolaus Copernicus UniversityBydgoszczPoland

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