NEAREST-NEIGHBOR THERMODYNAMIC PARAMETERS FOR INTERNAL G-CENTER-DOT-AMISMATCHES IN DNA

Thermodynamics of 22 oligonucleotides with internal single G.A mismatc hes dissolved in 1 M NaCl were determined from absorbance versus tempe rature melting curves. These data, combined with five literature seque nces. were used to derive nearest-neighbor thermodynamic parameters fo r seven linearly independent trimer sequences with internal G.T mismat ches 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 de viations of 4.4%, 7.4%: 8.0%, and 1.5 degrees C, respectively, The nea rest-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 dep endent.