Elucidation of the mechanism of single-stranded DNA interaction with methylene blue: A spectroscopic approach

The interaction of photosensitizer methylene blue (MB) with single stranded oligonucleotides of composition AAA-AAA-AAA (A9), CCC-CCC-CCC (C9), GGG-GGG-GGG (G9), and TTT-TTT-TTT (T9) has been studied using UV-vis and fluorescence spectroscopies. The quenching effect of single stranded G9 over MB is favored over the other sequences. The analysis of the fluorescence data by Benesi-Hildebrand plot shows that MB forms 1:1 complex with G9. Results from spectroscopic experiments, Stern-Volmer and van't Hoff plots are consistent with a principal contribution of the static quenching on the overall quenching mechanism and with the electrostatic binding mode of MB-single stranded G9 system. A quantum chemical modeling at DFT//B3LYP/6-31G(d,p) level confirms the experimental results. Asides from providing an insight into the underlying mechanism of the interaction between methylene blue and DNA, these results can be exploited for the design of novel DNA sensors using photoactive labels.