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

Result code in 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>
Alternative codes found
RIV/60076658:12110/10:00012209 RIV/60076658:12640/10:00012200
Result on the web
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DOI - Digital Object Identifier
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Result language
angličtina
Original language name
A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics
Original language description
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.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year
2010
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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