Base pair specificity and energetics of binding of the phenazinium molecules phenosafranine and safranine-O to deoxyribonucleic acids: a comparative study

Abstract

The base specificity and energetics of DNA binding of the phenazinium dyes phenosafranine and safranine-O have been studied using various biophysical tools. The guanine-cytosine base specificity of both compounds was established from binding affinity values and competition dialysis results and also from circular dichroism, thermal melting, and calorimetric studies. Both dyes bind to DNA with affinity of the order of 10(5) M(-1), but the values are significantly higher for the guanine-cytosine rich DNAs over adenine-thymine rich ones and for phenosafranine over safranine-O. Calorimetric studies revealed that the binding reactions were exothermic and favoured by negative enthalpy as well as predominantly large positive entropy contributions. The temperature dependence of enthalpy changes yielded negative heat capacity values, which were higher for phenosafranine, compared to safranine-O, suggesting substantial contribution from hydrophobic forces in the binding process. Enthalpy-entropy compensation behaviour was also observed for the binding of both dyes to DNAs, revealing the molecular aspects of the interaction. Taken together, the spectroscopic and calorimetric data reflect clearly the guanine-cytosine base specificity of these molecules and a stronger DNA binding of PSF over SO. The results also provide some insights into the role of a bulkier substituent in the phenazinium ring in the binding process.