Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment

Authors

  • Jiří Šponer,

    Corresponding author
    1. CEITEC—Central European Institute of Technology, Campus Bohunice, Czech Republic
    • Institute of Biophysics, Academy of Sciences of the Czech Republic, Czech Republic
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  • Judit E. Šponer,

    1. Institute of Biophysics, Academy of Sciences of the Czech Republic, Czech Republic
    2. CEITEC—Central European Institute of Technology, Campus Bohunice, Czech Republic
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  • Arnošt Mládek,

    1. Institute of Biophysics, Academy of Sciences of the Czech Republic, Czech Republic
    2. CEITEC—Central European Institute of Technology, Campus Bohunice, Czech Republic
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  • Petr Jurečka,

    1. Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, Czech Republic
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  • Pavel Banáš,

    1. Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, Czech Republic
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  • Michal Otyepka

    1. Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, Czech Republic
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Correspondence to: Jiří Šponer; e-mail: sponer@ncbr.muni.cz

ABSTRACT

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π–π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 978–988, 2013.

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