Number of the records: 1
A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics
- 1.
SYSNO ASEP 0351842 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics Author(s) Kabeláč, Martin (UOCHB-X)
Zimandl, F. (CZ)
Fessel, T. (CZ)
Chval, Z. (CZ)
Lankaš, Filip (UOCHB-X) RIDNumber of authors 5 Source Title Physical Chemistry Chemical Physics. - : Royal Society of Chemistry - ISSN 1463-9076
Roč. 12, č. 33 (2010), s. 9677-9684Number of pages 8 s. Language eng - English Country GB - United Kingdom Keywords rhodamine ; QSY 21 ; DNA Subject RIV CF - Physical ; Theoretical Chemistry R&D Projects LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) IAA400550808 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) CEZ AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000281007200014 DOI 10.1039/c004020g Annotation 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. 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 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 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Year of Publishing 2011
Number of the records: 1