Free energy contributions of G.cntdot.U and other terminal mismatches to helix stability

Abstract

Thermodynamic parameters of helix formation were measured spectroscopically for seven hexaribonucleotides containing a GC tetramer core and G.cntdot.U or other terminal mismatches. The free energies of helix formation are compared with those for the tetramer core alone and with those for the hexamer with six Watson-Crick base pairs. In 1 M NaCl, at 37.degree. C, the free energy of a terminal G.cntdot.U mismatch is about equal to that of the corresponding A.cntdot.U pair. Although other terminal mismatches studied add between -1.0 and -1.6 kcal/mol to .DELTA.G.degree.37 for helix formation, all are less stable than the corresponding Watson-Crick pairs. Comparisons of the stability increments for terminal G.cntdot.U mismatches and G.cntdot.C pairs suggests when stacking is weak the additional hydrogen bond in the G.cntdot.C pair adds roughly -1 kcal/mol to the favorable free energy of duplex formation.