Thermodynamics of small symmetrical internal loops in RNA: sequence, pH and ion effects

Abstract

Folding of single‐stranded RNA upon itself generates complex structures containing many bulges and loops along with A‐form helical regions. Specific symmetrical bulges in RNA exist in various biological structures, including leadzyme, thiamine pyrophosphate riboswitch and certain tRNAs. Small symmetrical loops in RNA show significant thermodynamic differences that are dependent on the closing base pairs and the base sequences of the internal loops. In this study, seven 2 x 2 symmetrical bulged‐RNA constructs were examined along with various control RNA. In 1 M KCl at pH 7.5, only small differences in RNA stability were observed, with construct being the least stable and being the most stable. In 1 M KCl at pH 5.5, the differences in stability were significantly greater, with construct being the least stable and the construct being the most stable. Magnesium ions had a modest effect on RNA stability in pH 7.5 conditions, with only a small gain in RNA stability (0.5 kcal/mol) seen for some constructs. In pH 5.5 and 9.5 mM Mg2+ ions, all bulged‐RNA constructs examined gained ~1 kcal/mol relative to 1 M salt, indicating protonation‐dependent bonding in the loops. The thermodynamic effects of varying concentrations of monovalent and divalent ions on the non‐canonical base pairs in the bulge and the effect of closing canonical base pairs will be presented. This work was funded by NSF MCB‐0621509 to NG.