Examining [2,2′-bipyridyl]-3,3′-diol as a possible DNA model base pair

Abstract

[2,2′-Bipyridyl]-3,3′-diol (BP(OH)2) is known to undergo excited state intramolecular double proton transfer in solution. Steady state absorption and fluorescence spectra of BP(OH)2 were studied here in solvents of varying polarity and hydrogen bonding capability, and in binary mixtures of p-dioxane/water in order to test its applicability as a model base pair. Unique absorption due to water solvation was observed in the region of 400-450 nm. Only the di-keto-tautomer fluoresces in all the solvents studied here. A large blue-shift in the fluorescence band due to intermolecular hydrogen bonding was observed in polar, protic solvents which increases with increasing solvent polarity. Results from the absorption spectra in the binary mixtures were fitted to a binding isotherm model and three water molecules were found to solvate each of the two hydrogen bonding centers in BP(OH)2. Molecular dynamics simulations were performed for a dodecamer duplex DNA containing BP(OH)2 as a model base pair in the center of the duplex. The results of the simulations indicate that BP(OH)2 can serve as a good mimic of a natural base pair with no major perturbation to the helical structure's stability. One of the two hydrogen bonds in BP(OH)2 resides in the major groove of the duplex DNA, whereas the other one is situated in the minor groove. The preferential stacking between the flanking base pairs of duplex DNA and its unique spectroscopic features in water make BP(OH)2 a potential probe for tautomerization in DNA and a possible sensor for water accessibility in the major and minor grooves of DNA. © 2006 Elsevier B.V. All rights reserved.