TY - JOUR
T1 - Examining [2,2′-bipyridyl]-3,3′-diol as a possible DNA model base pair
AU - Abou-Zied, Osama K.
N1 - Funding Information:
This work was supported by the Sultan Qaboos University (grant #IG/SCI/CHEM/05/03). The author would like to thank Prof. David Case of the Scripps Research Institute for providing a copy of the Amber 8 program.
PY - 2006/8/31
Y1 - 2006/8/31
N2 - [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.
AB - [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.
KW - Absorption
KW - Binary mixtures
KW - Fluorescence
KW - Molecular dynamics simulations
KW - [2,2′-Bipyridyl]-3,3′-diol
UR - http://www.scopus.com/inward/record.url?scp=33746361826&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33746361826&partnerID=8YFLogxK
U2 - 10.1016/j.jphotochem.2006.02.015
DO - 10.1016/j.jphotochem.2006.02.015
M3 - Article
AN - SCOPUS:33746361826
SN - 1010-6030
VL - 182
SP - 192
EP - 201
JO - Journal of Photochemistry and Photobiology A: Chemistry
JF - Journal of Photochemistry and Photobiology A: Chemistry
IS - 2
ER -