Abstract
AbstractSome organic dyes, derivatives of the 4‐(arylethynyl)‐7‐(4‐methoxyphenyl)‐2,1,3‐benzothiadiazoles (BTDs) bind strongly to double stranded DNA, exhibiting a strong increase in the fluorescence intensity. Due to this property, they were proposed as very sensitive probes for DNA detection and quantification. The details of the interaction mechanism, however, are unknown. In this work, we use docking and molecular dynamics simulations to study the interactions of these BTDs with DNA. We used a docking protocol where the receptor is a modified canonical oligonucleotide, with a gap, to sample intercalation and minor groove binding modes. Starting from several independent but energetically favorable docking poses, molecular dynamics simulations were carried out, investigating the ligand‐DNA interactions and the time evolution of the DNA structure. We observed, in agreement with experimental results, that the presence of the ethynyl spacer in the ligand stabilizes the intercalation binding mode, yielding strong interactions with DNA and large residence times. © 2012 Wiley Periodicals, Inc.
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