Strategies for Modeling Ligand Docking to Natural and Engineered RNA Structures

Abstract

5 UUUUUUU, where U 11 and U 5 are loops of 11 and 5 uridines, respectively. We used a combination of temperature-dependent UV spectroscopy and differential scanning calorimetric techniques to determine the unfolding thermodynamics of each pseudoknot. Additional UV melting experiments were done as a function of oligomer, salt and osmolyte concentrations to determine the transition molecularity, ion and water binding, respectively. In the 16-116 mM NaCl range, U-PsKn has a higher T M s and is thermodynamically more stable (by 12.3 kcal/ mol) than dU-PsKn. This large differential free energy contribution is driven by a differential favorable enthalpy contribution of 34.3 kcal/mol. In addition, U-PsKn immobilizes more counterions (by 0.3 per mol,) and water molecules (by 16 per mol), and unfolds with a higher heat capacity contribution (by 1.0 kcal/ o C-mol) than its DNA analog. Furthermore, the overall enthalpy is higher than the corresponding enthalpy of its double helical stem (estimated from nearestneighbors contributions), suggesting the longer U 11 loop could potentially form local UAU base-triplets with the adjacent A 7 /U 7 stem. We estimate U-PsKn forms 7 base-triplet stacks while dU-PsKn forms 4 base-triplet stacks. The overall results imply U-PsKn forms a more compact structure.