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Practical Aspects of Computational Chemistry pp 399–413Cite as

Conformational Flexibility of Pyrimidine Ring in Nucleic Acid Bases

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Abstract

Nucleic acid bases (NABs) have been considered for many years to be planar and conformationally rigid. However, recently, two possible sources of nucleobases nonplanarity have been found. Ab initio quantum-chemical calculations using large basis sets augmented by inclusion of electron correlation and recent experimental studies revealed that amino groups in isolated cytosine, guanine, and adenine adopt a nonplanar trigonal-pyramidal configuration. Since the values of amino group inversion barriers do not exceed approximately 1 kcal mol−1, this group possesses rather flexible geometry. A different source of nonplanarity of nucleobases originates from the high deformability of the pyrimidine ring. Transition of such a ring in uracil, thymine, cytosine, and guanine molecules from a planar equilibrium conformation to a sofa configuration characterized by a relevant torsion angle of ±20° entails an increase of energy by less than 1.5 kcal mol−1. Therefore, at room temperature, certain fraction of isolated DNA bases should possess nonplanar structure of the heterocyclic ring. This review summarizes recent theoretical studies on the flexibility of the NABs.

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Acknowledgments

This work was supported by NSF CREST Interdisciplinary Nanotoxicity Center (grant number HRD-0833178).

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Authors and Affiliations

  1. NSF CREST Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 17910, 1325 Lynch str., Jackson, MS, 39217, USA

    Oleg V. Shishkin, Leonid Gorb & Jerzy Leszczynski

  2. Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, 150 Zabolotnogo St., Kyiv, 03143, Ukraine

    Leonid Gorb

  3. STC “Institute for Single Crystals”, National Academy of Science of Ukraine, 60 Lenina ave., Kharkiv, 61001, Ukraine

    Oleg V. Shishkin

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  1. Oleg V. Shishkin
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  2. Leonid Gorb
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  3. Jerzy Leszczynski
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Correspondence to Jerzy Leszczynski .

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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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Shishkin, O.V., Gorb, L., Leszczynski, J. (2009). Conformational Flexibility of Pyrimidine Ring in Nucleic Acid Bases. In: Leszczynski, J., Shukla, M. (eds) Practical Aspects of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2687-3_21

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