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Practical Aspects of Computational Chemistry pp 387–397Cite as

Nucleic Acid Base Complexes: Elucidation of the Physical Origins of Their Stability

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Abstract

Nucleic acids and proteins are biochemically important complexes responsible for heirdom and miscellaneous enzymatic cellular processes. Thus, the understanding of the physical origins of their stability, i.e., the nature of intermolecular interactions, is crucial for the interpretation of various biochemical processes. The intercalation of drugs into DNA may serve as an illuminating example. The most accurate and reliable framework for the analysis of intermolecular interactions is provided by the quantum mechanics. In general, two distinct approaches are usually used for the evaluation of interaction energies, namely the supermolecular approach and the perturbation theory. While the former explains the interaction energy as small difference between the values of the energy of the whole complex and the sum of energies of the monomers, the latter allows for direct calculation of contributions with a clear physical interpretation. Unfortunately, the majority of studies of the nucleic acid base complexes had either shown little concern for the elucidation of the nature of interactions or analyzed this aspect qualitatively. The present contribution is especially aimed at the compact and comprehensible presentation of the most important observations made on the physical origins of nucleic acid base pairs’ stability. Throughout, we shall support the discussion by our own findings in this fascinating area.

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Acknowledgements

The authors are grateful to Dr. Robert W. Gora for the access to the modified version of the GAMESS US code. This work was supported by computational grants from WCSS (Wroclaw Centre for Networking and Supercomputing) and ACK Cyfronet. The allocation of computing time is greatly appreciated.

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Authors and Affiliations

  1. Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635, Athens, Greece

    Żaneta Czyżnikowska, Robert Zaleśny & Manthos G. Papadopoulos

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  1. Żaneta Czyżnikowska
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  2. Robert Zaleśny
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  3. Manthos G. Papadopoulos
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Correspondence to Żaneta Czyżnikowska .

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Editors and Affiliations

  1. Dept. Chemistry, Jackson State University, J. R. Lynch St. 1325, Jackson, 39217, U.S.A.

    Jerzy Leszczynski

  2. Dept. Chemistry, Jackson State University, J. R. Lynch St. 1325, Jackson, 39217, U.S.A.

    Manoj K. Shukla

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Czyżnikowska, Ż., Zaleśny, R., Papadopoulos, M.G. (2009). Nucleic Acid Base Complexes: Elucidation of the Physical Origins of Their Stability. In: Leszczynski, J., Shukla, M. (eds) Practical Aspects of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2687-3_20

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