Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability

摘要

The effect of loop sequence and identity of the duplex base pair closing the loop on the stability of 28 DNA hairpins was investigated by monitoring their temperature-induced melting transitions in buffered 115 mM Na+ solvent by UV spectroscopy and differential scanning calorimetry. The melting temperatures of the molecules were found to range from 32.4 to 60.5 °C and to be concentration independent over strand concentrations of 0.5 to 260 μM, indicating that the melting transitions are unimolecular. Comparisons between model independent calorimetric values and thermodynamic parameters evaluated assuming a two-state model reveal that 10 of the 28 hairpins display non-two-state melting behavior.