Melting studies of short DNA hairpins containing the universal base 5-nitroindole

Effects of the universal base 5-nitroindole on the thermodynamic stability of DNA hairpins having a 6 bp stem and four base loops were investigated by optical absorbance and differential scanning calorimetry techniques. Melti ng studies were conducted in buffer containing 115 mM Na+. Five different m odified versions of DNA hairpins containing a 5-nitroindole base or bases s ubstituted at different positions in the stem and loop regions were examine d. Thermodynamic parameters of the melting transitions estimated from a two -state analysis of optical melting curves and measured directly by calorime try revealed that the presence of 5-nitroindole bases in the duplex stem or loop regions of short DNA hairpins significantly affects both their enthal pic and entropic melting components in a compensating manner, while the tra nsition free energy varies linearly with the transition temperature. The ca lorimetrically determined enthalpy and entropy values of the modified hairp ins were considerably smaller (43-53%) than the two-state optical parameter s, suggesting that solvent effects may be significant in the melting proces ses of these hairpins. Results of circular dichroism measurements also reve aled slight differences between the modified hairpins and the control in bo th the duplex and melted states, suggesting subtle structural differences b etween the control and DNA hairpins containing a 5-nitroindole base or base s.