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

0351842 - ÚOCHB 2011 RIV GB eng J - Článek v odborném periodiku
Kabeláč, Martin - Zimandl, F. - Fessel, T. - Chval, Z. - Lankaš, Filip
A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics.
Physical Chemistry Chemical Physics. Roč. 12, č. 33 (2010), s. 9677-9684. ISSN 1463-9076. E-ISSN 1463-9084
Grant CEP: GA MŠMT LC512; GA AV ČR IAA400550808
Výzkumný záměr: CEZ:AV0Z40550506
Klíčová slova: rhodamine * QSY 21 * DNA
Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
Impakt faktor: 3.454, rok: 2010

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.
Trvalý link: http://hdl.handle.net/11104/0191498