Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop

All 64 possible thermodynamic parameters for a single-bulge loop in the middle of a sequence were derived from optical melting studies. The relative stability of a single bulge depended on both the type of bulged base and its flanking base pairs. The contribution of the single bulge to helix stability ranged from 3.69 kcal/mol for a TAT bulge to - 1.05 kcal/mol for an ACC bulge. Thermodynamics for 10 sequences with a GTG bulge were determined to test the applicability of the nearest-neighbor model to a single-bulge loop. Thermodynamic parameters for the GTG bulge and Watson-Crick base pairs predict DeltaG(37)degrees, DeltaHdegrees DeltaSdegrees and T-M(50muM) values with average deviations of 3.0%, 4.3%, 4.7%, and 0.9 degreesC, respectively. The prediction accuracy was within the limits of what can be expected for a nearestneighbor model. This certified that the thermodynamics for single-bulge loops can be estimated adequately using a nearest-neighbor model.