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Statements

Subject Item
n2:RIV%2F61989592%3A15310%2F12%3A33142854%21RIV13-MSM-15310___
rdf:type
skos:Concept n14:Vysledek
dcterms:description
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 selfcleavage 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. 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 selfcleavage 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.
dcterms:title
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
skos:prefLabel
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
skos:notation
RIV/61989592:15310/12:33142854!RIV13-MSM-15310___
n14:predkladatel
n21:orjk%3A15310
n3:aktivita
n4:Z n4:P
n3:aktivity
P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(GA203/09/1476), P(GAP208/10/2302), P(GAP208/11/1822), P(GAP208/12/1878), P(GBP305/12/G034), P(GD203/09/H046), Z(AV0Z50040702), Z(MSM6046137302)
n3:cisloPeriodika
44
n3:dodaniDat
n16:2013
n3:domaciTvurceVysledku
n9:3151948 n9:3843912 n9:1878220 n9:7638000
n3:druhVysledku
n18:J
n3:duvernostUdaju
n20:S
n3:entitaPredkladatele
n8:predkladatel
n3:idSjednocenehoVysledku
131752
n3:idVysledku
RIV/61989592:15310/12:33142854
n3:jazykVysledku
n10:eng
n3:klicovaSlova
self-cleaving ribozymes; main-group thermochemistry; intrinsic conformational properties; single-strand breaks; intramolecular hydrogen-bonds; density-functional calculations; nucleic-acid backbone; molecular-dynamics simulations; hepatitis-delta-virus
n3:klicoveSlovo
n6:hepatitis-delta-virus n6:density-functional%20calculations n6:single-strand%20breaks n6:nucleic-acid%20backbone n6:molecular-dynamics%20simulations n6:self-cleaving%20ribozymes n6:main-group%20thermochemistry n6:intramolecular%20hydrogen-bonds n6:intrinsic%20conformational%20properties
n3:kodStatuVydavatele
GB - Spojené království Velké Británie a Severního Irska
n3:kontrolniKodProRIV
[251CA4469AAF]
n3:nazevZdroje
Physical Chemistry Chemical Physics
n3:obor
n15:CF
n3:pocetDomacichTvurcuVysledku
4
n3:pocetTvurcuVysledku
8
n3:projekt
n11:GA203%2F09%2F1476 n11:GD203%2F09%2FH046 n11:GBP305%2F12%2FG034 n11:GAP208%2F12%2F1878 n11:GAP208%2F11%2F1822 n11:ED1.1.00%2F02.0068 n11:ED2.1.00%2F03.0058 n11:GAP208%2F10%2F2302
n3:rokUplatneniVysledku
n16:2012
n3:svazekPeriodika
14
n3:tvurceVysledku
Banáš, Pavel Mládek, Arnošt Zgarbová, Marie Otyepka, Michal Jurečka, Petr Šponerová, Judit E. Svozil, Daniel Šponer, Jiří
n3:wos
000310153300002
n3:zamer
n5:MSM6046137302 n5:AV0Z50040702
s:issn
1463-9076
s:numberOfPages
21
n13:doi
10.1039/c2cp41987d
n17:organizacniJednotka
15310