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.

Základní údaje

Originální název

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

Autoři

ŠPONER, Jiří (203 Česká republika, garant, domácí), Judit ŠPONEROVÁ (348 Maďarsko, domácí), Arnošt MLÁDEK (203 Česká republika, domácí), Petr JURECKA (203 Česká republika), Pavel BANÁŠ (203 Česká republika) a Michal OTYEPKA (203 Česká republika)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.288

Kód RIV

RIV/00216224:14740/13:00072152

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000325089800007

Klíčová slova anglicky

stacking; nucleic acids; quantum-chemical calculations

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 10. 4. 2014 04:48, Olga Křížová

Anotace

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

ŠPONER, Jiří, Judit ŠPONEROVÁ, Arnošt MLÁDEK, Petr JURECKA, Pavel BANÁŠ a Michal OTYEPKA. Nature and Magnitude of Aromatic Base Stacking in DNA and RNA: Quantum Chemistry, Molecular Mechanics, and Experiment. Biopolymers. Hoboken: WILEY-BLACKWELL, 2013, roč. 99, č. 12, s. 978-988. ISSN 0006-3525. Dostupné z: 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 a 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, roč.~99, č.~12, s.~978-988. ISSN~0006-3525. Dostupné z: https://dx.doi.org/10.1002/bip.22322.

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