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

Abstract

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 (Delta Gdegrees(loop)) of the 2 x 2 loops were positive, and showed relatively small differences between the two closing base pair environments. Assuming temperature-independent enthalpy changes for the transitions, (Delta Gdegrees(loop)) for the 2 x 2 loops varied from 0.9 to 1.9 kcal/mol in 1 M Na(+) at 37 degrees 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 (DeltaC(p)) associated with the transitions of two RNA duplexes was estimated by plotting DeltaH degrees and DeltaS degrees evaluated at different strand concentrations as a function of T(m) and ln T(m), respectively. The average DeltaC(p) 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 degrees C of the 10 bp control RNA duplexes by 0.3-0.6 kcal/mol, which may increase Delta Gdegrees(loop) values by similar amounts.

Folding Kinetics for the Conformational Switch between Alternative RNA Structures

“…Thermodynamics studies suggest that RNA folding may be accompanied with a change in the heat capacity Δ C P ,34, 35 resulting in a temperature dependence of the enthalpy and entropy parameters: $$\mathrm{\Delta }{C}_P={false[\frac{\partial \mathrm{normal\Delta }H}{\partial T}false]}_P={false[T\frac{\partial \mathrm{normal\Delta }S}{\partial T}false]}_P$$…”

Computational approaches for RNA energy parameter estimation

“…Secondly, we collected a thermodynamic set denoted by T-Full that contains data from 1291 optical melting experiments, published in 53 research articles Sugimoto et al 1986Sugimoto et al , 1987Uhlenbeck 1988, 1989;Longfellow et al 1990;SantaLucia et al 1990SantaLucia et al , 1991aAntao et al 1991;He et al 1991;Peritz et al 1991;Antao and Tinoco 1992;Serra et al 1993Serra et al , 1994Serra et al , 1997Serra et al , 2004Walter et al 1994;Morse and Draper 1995;Wu et al 1995;Laing and Hall 1996;McDowell and Turner 1996;McDowell et al 1997;Schroeder et al 1996Schroeder et al , 2003Xia et al 1997Xia et al , 1998Giese et al 1998;Kierzek et al 1999;Meroueh and Chow 1999;Dale et al 2000;Turner 2000, 2001;Burkard et al 2001;Diamond et al 2001;Mathews and Turner 2002;Proctor et al 2002;Znosko et al 2002Znosko et al , 2004Chen et al 2004Chen et al , 2005Mathews et al 2004;Vecenie and Serra 2004;Bourdélat-Parks and Wartell 2005;…”

A U⋅U Pair‐to‐U⋅C Pair Mutation‐Induced RNA Native Structure Destabilisation and Stretching‐Force‐Induced RNA Misfolding

“…Typically,w hen adjacent to as tem, aU ·Upairist hermodynamically more stable (by about 0.5-1 kcal mol À1 )t han aU ·Cp air,a sr evealed by ensemblet hermalm elting studies. [8,9,15,21,[33][34][35][36] However,l ittle is known about how U·Ua nd U·Cb ase pairs affect the mechanical properties and (un)folding dynamics of an RNA structure.…”