DNA Microenvironment Monitored by Controlling Redox Blinking.

The rate of a bimolecular reaction between a fluorophore and a freely diffusing molecule in the solvent depends on the accessibility of the fluorophore for collision with the molecule. We previously reported that the observation of blinking, caused by the formation of R6G in the excited triplet state ((3) R6G*) and its quenching reaction with O2 , allowed us to monitor the DNA conformational changes between a duplex and a hairpin. However, the small molecular size of O2 hampered sensitive monitoring of the microenvironment changes around R6G. In this study, we control redox blinking by adding a reductant ascorbic acid 2-phosphate (VcP), which converts (3) R6G* into the radical anion form R6G(.-) , and by adding a bulky oxidant FeDTPA. The bimolecular electron-transfer rate between R6G(.-) and bulky FeDTPA was more strongly affected by microenvironment changes around R6G, compared with that between (3) R6G* and the smaller O2 . This allowed us to monitor subtle DNA conformational changes caused by a single different nucleotide.