About: Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://pubs.acs.org/doi/abs/10.1021/ja402525c
Description	We provide theoretical predictions of the intrinsic stability of different arrangements of guanine quadruplex (G-DNA) stems. Most computational studies of nucleic acids have applied Molecular Mechanics (MM) approaches using simple pairwise-additive force fields. The principle limitation of such calculations is the highly approximate nature of the force fields. In this study, we for the first time apply accurate QM computations (DFT-D3 with large atomic orbital basis sets) to essentially complete DNA building blocks, seven different folds of the cation stabilized two quartet G-DNA stem, each having more than 250 atoms. The solvent effects are approximated by COSMO continuum solvent We reveal sizable differences between MM and QM descriptions of relative energies of different G-DNA stems, which apparently reflect approximations of the DNA force field. We provide theoretical predictions of the intrinsic stability of different arrangements of guanine quadruplex (G-DNA) stems. Most computational studies of nucleic acids have applied Molecular Mechanics (MM) approaches using simple pairwise-additive force fields. The principle limitation of such calculations is the highly approximate nature of the force fields. In this study, we for the first time apply accurate QM computations (DFT-D3 with large atomic orbital basis sets) to essentially complete DNA building blocks, seven different folds of the cation stabilized two quartet G-DNA stem, each having more than 250 atoms. The solvent effects are approximated by COSMO continuum solvent We reveal sizable differences between MM and QM descriptions of relative energies of different G-DNA stems, which apparently reflect approximations of the DNA force field. (en)
Title	Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations (en)
skos:prefLabel	Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations (en)
skos:notation	RIV/00216224:14740/13:00069530!RIV14-MSM-14740___
http://linked.open...avai/riv/aktivita	I P Z
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(GAP208/11/1822), Z(AV0Z50040702)
http://linked.open...iv/cisloPeriodika	26
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Šponer, Jiří Špačková, Naďa Mládek, Arnošt
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	102230
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/13:00069530
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	DENSITY-FUNCTIONAL THEORY; MOLECULAR-DYNAMICS SIMULATIONS; SUGAR-PHOSPHATE BACKBONE; APPROXIMATE COULOMB POTENTIALS; HUMAN TELOMERIC QUADRUPLEXES; ZETA VALENCE QUALITY; AUXILIARY BASIS-SETS; AMBER FORCE-FIELD; NUCLEIC-ACIDS; CRYSTAL-STRUCTURE (en)
http://linked.open.../riv/klicoveSlovo	CRYSTAL-STRUCTURE DENSITY-FUNCTIONAL THEORY AMBER FORCE-FIELD AUXILIARY BASIS-SETS HUMAN TELOMERIC QUADRUPLEXES SUGAR-PHOSPHATE BACKBONE ZETA VALENCE QUALITY NUCLEIC-ACIDS MOLECULAR-DYNAMICS SIMULATIONS APPROXIMATE COULOMB POTENTIALS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[A4F509DACE58]
http://linked.open...i/riv/nazevZdroje	Journal of the American Chemical Society
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Central european institute of technology Structure and dynamics of DNA. Advanced computational studies.
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	135
http://linked.open...iv/tvurceVysledku	Šponer, Jiří Mládek, Arnošt Cheatham, Thomas E. Cang, Xiaohui H. Grimme, Stefan Špačková, Naděžda
http://linked.open...ain/vavai/riv/wos	000321541800040
http://linked.open...n/vavai/riv/zamer	Genome and epigenome: 1D and 3D Structure, Dynamics, Interactions with Proteins and Functions
issn	0002-7863
number of pages	12 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ja402525c
http://localhost/t...ganizacniJednotka	14740

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