Journal
BIOCHEMISTRY
Volume 43, Issue 22, Pages 7143-7150Publisher
AMER CHEMICAL SOC
DOI: 10.1021/bi036188r
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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.
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