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Thermodynamics of RNA Duplexes with Tandem Mismatches Containing a Uracil-Uracil Pair Flanked by C·G/G·C or G·C/A·U Closing Base Pairs

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journal contribution
posted on 20.12.2005, 00:00 by Brooke N. Bourdélat-Parks, Roger M. Wartell
The thermodynamics governing the denaturation of RNA duplexes containing 8 bp and a central tandem mismatch or 10 bp were evaluated using UV absorbance melting curves. Each of the eight tandem mismatches that were examined had one U-U pair adjacent to another noncanonical base pair. They were examined in two different RNA duplex environments, one with the tandem mismatch closed by G·C base pairs and the other with G·C and A·U closing base pairs. The free energy increments ( ) of the 2 × 2 loops were positive, and showed relatively small differences between the two closing base pair environments. Assuming temperature-independent enthalpy changes for the transitions, for the 2 × 2 loops varied from 0.9 to 1.9 kcal/mol in 1 M Na+ at 37 °C. Most values were within 0.8 kcal/mol of previously estimated values; however, a few sequences differed by 1.2−2.0 kcal/mol. Single strands employed to form the RNA duplexes exhibited small noncooperative absorbance increases with temperature or transitions indicative of partial self-complementary duplexes. One strand formed a partial self-complementary duplex that was more stable than the tandem mismatch duplexes it formed. Transitions of the RNA duplexes were analyzed using equations that included the coupled equilibrium of self-complementary duplex and non-self-complementary duplex denaturation. The average heat capacity change (ΔCp) associated with the transitions of two RNA duplexes was estimated by plotting ΔH° and ΔS° evaluated at different strand concentrations as a function of Tm and ln Tm, respectively. The average ΔCp was 70 ± 5 cal K-1 (mol of base pairs)-1. Consideration of this heat capacity change reduced the free energy of formation at 37 °C of the 10 bp control RNA duplexes by 0.3−0.6 kcal/mol, which may increase values by similar amounts.

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