About: A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Molecular dynamics (MD) simulations and ab initio quantum chemical calculations were employed to investigate the structure, dynamics and interactions of the QSY 21 nonfluorescent quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. In the first motif, the central xanthene ring is stacked on one base of the adjacent cytosine-guanine DNA base pair, whereas one of the 2,3-dihydro-1-indolyl aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA base pair is mediated only by one of the side rings. Several transitions between the motifs are observed during a MD simulation. The ab initio calculations show that none of these motifs is energetically preferred. Two binding motifs were found also for Rhodamine 6G, with the xanthene ring stacked predominantly either on the cytosine or on the guanine. These results suggest that the side rings of QSY 21 play a crucial role in its stacking o Molecular dynamics (MD) simulations and ab initio quantum chemical calculations were employed to investigate the structure, dynamics and interactions of the QSY 21 nonfluorescent quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. In the first motif, the central xanthene ring is stacked on one base of the adjacent cytosine-guanine DNA base pair, whereas one of the 2,3-dihydro-1-indolyl aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA base pair is mediated only by one of the side rings. Several transitions between the motifs are observed during a MD simulation. The ab initio calculations show that none of these motifs is energetically preferred. Two binding motifs were found also for Rhodamine 6G, with the xanthene ring stacked predominantly either on the cytosine or on the guanine. These results suggest that the side rings of QSY 21 play a crucial role in its stacking o (en)
Title	A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics (en)
skos:prefLabel	A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics (en)
skos:notation	RIV/60076658:12640/10:00012200!RIV11-GA0-12640___
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(GC204/09/J010), P(IAA400550808), P(LC512), S, Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	33
http://linked.open...vai/riv/dodaniDat	2011
http://linked.open...aciTvurceVysledku	Fessl, Tomáš Chval, Zdeněk
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	Jihočeská univerzita v Českých Budějovicích / Ústav fyzikální biologie
http://linked.open...dnocenehoVysledku	244519
http://linked.open...ai/riv/idVysledku	RIV/60076658:12640/10:00012200
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	AMBER FORCE-FIELD; 6G-DNA COMPLEXES; NUCLEIC-ACIDS; BIPHENYL; SIMULATIONS; MICROARRAY; ASSAY (en)
http://linked.open.../riv/klicoveSlovo	ASSAY AMBER FORCE-FIELD NUCLEIC-ACIDS SIMULATIONS MICROARRAY 6G-DNA COMPLEXES BIPHENYL
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[8858B882B132]
http://linked.open...i/riv/nazevZdroje	Physical Chemistry Chemical Physics
http://linked.open...in/vavai/riv/obor	BO
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	5 (xsd:int)
http://linked.open...vavai/riv/projekt	Modeling of DNA-chip hybridization in real conditions Hydration and solvation of building blocks of biopolymers Center for biomolecules and complex molecular systems
http://linked.open...UplatneniVysledku	2010
http://linked.open...v/svazekPeriodika	12
http://linked.open...iv/tvurceVysledku	Chval, Zdeněk Fessl, Tomáš Kabelac, Martin Lankas, Filip Zimandl, Filip
http://linked.open...ain/vavai/riv/wos	000281007200014
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	1463-9076
number of pages	8 (xsd:int)
http://localhost/t...ganizacniJednotka	12640
is http://linked.open...avai/riv/vysledek of	A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics

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