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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F10%3A00351842" target="_blank" >RIV/61388963:_____/10:00351842 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60076658:12110/10:00012209 RIV/60076658:12640/10:00012200

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

Molecular dynamics (MD) simulations and ab initio calculations were employed to investigate the structure and dynamics of the QSY 21 quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. Inthe first motif, the central xanthene ring is stacked on one base of the adjacent cytosine?guanine DNA base pair, whereas one of the aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA basepair 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 preferred. Two binding motifs were found also for Rhodamine, with the xanthene ring stacked either on the cytosine or on the guanine. The results suggest that the side rings of QSY 21 play a crucial role in its stacking on the DNA and indicate novel binding mode absent in the case of Rhodamine 6G.

Název v anglickém jazyce

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

Popis výsledku anglicky

Molecular dynamics (MD) simulations and ab initio calculations were employed to investigate the structure and dynamics of the QSY 21 quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. Inthe first motif, the central xanthene ring is stacked on one base of the adjacent cytosine?guanine DNA base pair, whereas one of the aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA basepair 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 preferred. Two binding motifs were found also for Rhodamine, with the xanthene ring stacked either on the cytosine or on the guanine. The results suggest that the side rings of QSY 21 play a crucial role in its stacking on the DNA and indicate novel binding mode absent in the case of Rhodamine 6G.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2010

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Physical Chemistry Chemical Physics

ISSN

1463-9076

e-ISSN

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Svazek periodika

12

Číslo periodika v rámci svazku

33

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

8

Strana od-do

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Kód UT WoS článku

000281007200014

EID výsledku v databázi Scopus

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