Nature and Magnitude of Aromatic Base Stacking in DNA and RNA:
Quantum Chemistry, Molecular Mechanics, and Experiment

J 2013

Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Petr JURECKA, Pavel BANÁŠ et. al.

Basic information

Original name

Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment

Authors

ŠPONER, Jiří (203 Czech Republic, guarantor, belonging to the institution), Judit ŠPONEROVÁ (348 Hungary, belonging to the institution), Arnošt MLÁDEK (203 Czech Republic, belonging to the institution), Petr JURECKA (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic) and Michal OTYEPKA (203 Czech Republic)

Edition

Biopolymers, Hoboken, WILEY-BLACKWELL, 2013, 0006-3525

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 2.288

RIV identification code

RIV/00216224:14740/13:00072152

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1002/bip.22322

UT WoS

000325089800007

Keywords in English

stacking; nucleic acids; quantum-chemical calculations

Abstract

V originále

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 - energy term associated with the delocalized 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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Petr JURECKA, Pavel BANÁŠ and Michal OTYEPKA. Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. Biopolymers. Hoboken: WILEY-BLACKWELL, 2013, vol. 99, No 12, p. 978-988. ISSN 0006-3525. Available from: https://dx.doi.org/10.1002/bip.22322.

@article{1165570,
   author = {Šponer, Jiří and Šponerová, Judit and Mládek, Arnošt and Jurecka, Petr and Banáš, Pavel and Otyepka, Michal},
   article_location = {Hoboken},
   article_number = {12},
   doi = {http://dx.doi.org/10.1002/bip.22322},
   keywords = {stacking; nucleic acids; quantum-chemical calculations},
   language = {eng},
   issn = {0006-3525},
   journal = {Biopolymers},
   title = {Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment},
   volume = {99},
   year = {2013}
}

TY  - JOUR
ID  - 1165570
AU  - Šponer, Jiří - Šponerová, Judit - Mládek, Arnošt - Jurecka, Petr - Banáš, Pavel - Otyepka, Michal
PY  - 2013
TI  - Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment
JF  - Biopolymers
VL  - 99
IS  - 12
SP  - 978-988
EP  - 978-988
PB  - WILEY-BLACKWELL
SN  - 00063525
KW  - stacking
KW  - nucleic acids
KW  - quantum-chemical calculations
N2  - 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 - energy term associated with the delocalized 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.
ER  -

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Petr JURECKA, Pavel BANÁŠ and Michal OTYEPKA. Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. \textit{Biopolymers}. Hoboken: WILEY-BLACKWELL, 2013, vol.~99, No~12, p.~978-988. ISSN~0006-3525. Available from: https://dx.doi.org/10.1002/bip.22322.

Detailed Information on Publication Record