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Computational Modeling of DNA and RNA Fragments

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Handbook of Computational Chemistry

Abstract

A comprehensive analysis of the benefits and pitfalls of quantum chemical methods used to determine the structures, properties, and functions of DNA and RNA fragments is presented. Main emphasis is given to the application of different ab initio quantum chemical methods. An overview of computations reveals that quantum chemical methods provide an important means to investigate structures and interactions in nucleic acids. However, judicious selection of computational approach is necessary, depending upon the nature of the problem under investigation.

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Acknowledgments

JS acknowledges the support from the Grant Agency of the Academy of Sciences of the Czech Republic (grant IAA400040802), Grant Agency of the Czech Republic (grant 203/09/1476), Ministry of Education of the Czech Republic (LC06030), and Academy of Sciences of the Czech Republic (grants AV0Z50040507 and AV0Z50040702). MKS and JL are thankful for supports from NSF-CREST (grant HRD-0833178) and NSF EPSCoR (grant 362492-190200-01\NSFEPS-0903787) and computational support from Mississippi Center for Supercomputing Research (MCSR).

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Authors and Affiliations

  1. Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic

    Jiří Šponer

  2. US Army Engineer Research and Development Center, 39180, Vicksburg, MS, USA

    Manoj K. Shukla

  3. Department of Chemistry and Biochemistry, Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, MS, 39217, USA

    Jing Wang & Jerzy Leszczynski

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  1. Jiří Šponer
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  2. Manoj K. Shukla
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  3. Jing Wang
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  4. Jerzy Leszczynski
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Corresponding author

Correspondence to Jiří Šponer .

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Editors and Affiliations

  1. Department of Chemistry and Biochemistry, Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi, USA

    Jerzy Leszczynski

  2. Faculty of Chemistry, Nicolaus Copernicus University, Toruń, Poland

    Anna Kaczmarek-Kedziera

  3. Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Tomasz Puzyn

  4. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Manthos G. Papadopoulos

  5. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Heribert Reis

  6. US Army Engineer Research and Development Center, Vicksburg, Mississippi, USA

    Manoj K. Shukla

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Šponer, J., Shukla, M.K., Wang, J., Leszczynski, J. (2017). Computational Modeling of DNA and RNA Fragments. In: Leszczynski, J., Kaczmarek-Kedziera, A., Puzyn, T., G. Papadopoulos, M., Reis, H., K. Shukla, M. (eds) Handbook of Computational Chemistry. Springer, Cham. https://doi.org/10.1007/978-3-319-27282-5_35

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