Nearest neighbor thermodynamic parameters for internal G•A mismatches in DNA

Thermodynamics of 22 oligonucleotides with internal single G.A mismatches dissolved in 1 M NaCl were determined from absorbance versus temperature melting curves. These data, combined with five literature sequences. were used to derive nearest-neighbor thermodynamic parameters for seven linearly independent trimer sequences with internal G.T mismatches and Watson-Crick flanking base pairs, The G.A mismatch parameters predict Delta G(37)(o), Delta H-o, Delta S-o, and T-M With average deviations of 4.4%, 7.4%: 8.0%, and 1.5 degrees C, respectively, The nearest-neighbor parameters show that G.A mismatch stability is strongly context dependent, and Delta G(37)(o); ranges from +1.16 kcal/mol for TGA/AAT to -0.78 kcal/mol for GGC/CAG. In addition, one-dimensional H-1 NMR spectra show that the G.A pairing,geometry is pH and context dependent.