Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA

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Abstract
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·A mismatches and Watson−Crick flanking base pairs. The G·A mismatch parameters predict ΔG°37, ΔH°, ΔS°, and TM with average deviations of 4.4%, 7.4%, 8.0%, and 1.5 °C, respectively. The nearest-neighbor parameters show that G·A mismatch stability is strongly context dependent, and ΔG°37 ranges from +1.16 kcal/mol for TGA/AAT to −0.78 kcal/mol for GGC/CAG. In addition, one-dimensional 1H NMR spectra show that the G·A pairing geometry is pH and context dependent.