ŠPONER, Jiří, Arnošt MLÁDEK, Judit ŠPONEROVÁ, Daniel SVOZIL, Marie ZGARBOVÁ, Pavel BANÁŠ, Petr JUREČKA and Michal OTYEPKA. The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. PHYSICAL CHEMISTRY CHEMICAL PHYSICS. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2012, vol. 14, No 44, p. 15257-15277. ISSN 1463-9076. doi:10.1039/c2cp41987d.
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Basic information
Original name The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
Authors ŠPONER, Jiří (203 Czech Republic, guarantor, belonging to the institution), Arnošt MLÁDEK (203 Czech Republic, belonging to the institution), Judit ŠPONEROVÁ (348 Hungary, belonging to the institution), Daniel SVOZIL (203 Czech Republic), Marie ZGARBOVÁ (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), Petr JUREČKA (203 Czech Republic) and Michal OTYEPKA (203 Czech Republic).
Edition PHYSICAL CHEMISTRY CHEMICAL PHYSICS, CAMBRIDGE, ROYAL SOC CHEMISTRY, 2012, 1463-9076.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10610 Biophysics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 3.829
RIV identification code RIV/00216224:14740/12:00057887
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1039/c2cp41987d
UT WoS 000310153300002
Keywords in English HEPATITIS-DELTA-VIRUS; MOLECULAR-DYNAMICS SIMULATIONS; NUCLEIC-ACID BACKBONE; DENSITY-FUNCTIONAL CALCULATIONS; INTRAMOLECULAR HYDROGEN-BONDS; SINGLE-STRAND BREAKS; INTRINSIC CONFORMATIONAL PROPERTIES; MAIN-GROUP THERMOCHEMISTRY; SELF-CLEAVING RIBOZYMES
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 28. 2. 2013 07:30.
Abstract
Knowledge of geometrical and physico-chemical properties of the sugar–phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure–energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar–phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar–phosphate backbone.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
GD203/09/H046, research and development projectName: Biochemie na rozcestí mezi in silico a in vitro
Investor: Czech Science Foundation
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