Binding of QSY 21 nonfluorescent quencher to DNA: Structure and dynamics

Molecular dynamics (MD) simulation and ab initio quantum mechanical calculations were employed to investigate the structure and dynamics of binding of QSY 21 nonfluorescent quencher to B-DNA decamer. Two binding motifs were observed: 1. Central xanthone ring of QSY 21 dye is oriented paralelly with the nearest DNA base pair and the complex is stabilized by stacking interaction between these two components. This binding motif has two substates. 2. The QSY 21 dye stacking interaction with the DNA bases is mediated only by one of the 2,3-dihydro-1-indolyl side rings of the dye. The ab initio calculations show that none of these binding motifs is energetically preferred. The less favorable stacking interaction between the dye and DNA bases in the second binding motif is probably compensated by advantageous interaction of dye and linker with DNA backbone.