About: Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

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About: Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations Goto Sponge NotDistinct Permalink

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na+ or K+). Large-scale molecular dynamics (MD) simulations have been utilized to study G-DNA quadruplex molecules containing mixed GCGC and all-guanine GGGG quartet layers. Incorporation of mixed GCGC quartets into G-DNA stems substantially enhances their sequence variability. The mixed quadruplexes form rigid assemblies that require integral monovalent cations for their stabilization. The interaction of cations with the all-guanine quartets is the leading contribution for the stability of the four-stranded assemblies, while the mixed quartets are rather tolerated within the structure. The simulations predict that two cations are preferred to stabilize a four-layer quadruplex stem composed of two GCGC and two all-guanine quartets. The distribution of cations in the structure is influenced by the position of the GCGC quartets within the quadruplex, the presence and arrangement of thymidine loops connecting the guanine/cytosine stretches forming the stems, and the cation type present (Na+ or K+). (en)
Title	Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations (en)
skos:prefLabel	Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations (en)
skos:notation	RIV/00216224:14310/01:00005554!RIV/2002/MSM/143102/N
http://linked.open.../vavai/riv/strany	3295
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(IAA4004002), P(LN00A016), Z(AV0Z4040901), Z(AV0Z5004920)
http://linked.open...iv/cisloPeriodika	14
http://linked.open...vai/riv/dodaniDat	2002
http://linked.open...aciTvurceVysledku	Šponer, Jiří Špačková, Naďa
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 / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	697444
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/01:00005554
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	PARTICLE-MESH-EWALD, STRANDED GUANINE TETRAPLEX, OXYTRICHA TELOMERIC DNA, BONDED G-TETRAD, CRYSTAL-STRUCTURE, NUCLEIC-ACIDS, FORCE-FIELD, ANGSTROM RESOLUTION, MINOR-GROOVE, SODIUM-IONS (en)
http://linked.open.../riv/klicoveSlovo	CRYSTAL-STRUCTURE FORCE-FIELD ANGSTROM RESOLUTION NUCLEIC-ACIDS BONDED G-TETRAD MINOR-GROOVE PARTICLE-MESH-EWALD SODIUM-IONS OXYTRICHA TELOMERIC DNA STRANDED GUANINE TETRAPLEX
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[4E09923D6674]
http://linked.open...i/riv/nazevZdroje	Journal of the American Chemical Society
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...ocetUcastnikuAkce	0 (xsd:int)
http://linked.open...nichUcastnikuAkce	0 (xsd:int)
http://linked.open...vavai/riv/projekt	BIOMOLECULAR CENTER Structure and interactions of nucleic acids and polypeptides at metal surfaces
http://linked.open...UplatneniVysledku	2001
http://linked.open...v/svazekPeriodika	123
http://linked.open...iv/tvurceVysledku	Šponer, Jiří Špačková, Naděžda Berger, Imre
http://linked.open...n/vavai/riv/zamer	Objasňování zákonitostí vztahů struktury a vlastností - zejména dynamiky a chemické reaktivity - látek a molekulárních systémů Biophysical properties of living systems and their changes under the influence of environmental factors
issn	0002-7863
number of pages	13 (xsd:int)
http://localhost/t...ganizacniJednotka	14310

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