Thermodynamic Examination of U6 ISL Bulged RNA

Abstract

There is a highly conserved bulge in the internal stem‐loop (ISL) of the U6 subunit of the spliceosome. It is responsible for spliseosome activation and catalysis. The U6 ISL bulge structure is pH dependent. At a pH around 7.0 the unpaired U80 bulged nucleotide is stacked within the helix causing a bend of approximately 25 degrees. At a lower pH U80 is flipped out into the major groove allowing the RNA to take up a conformation close to A‐form helix. There are several single mutations in this bulge that have proven lethal in yeast, and a few single mutations that exacerbate the lethality. Ion binding, pH effects, and the stability of various sequences involving the bulge will be studied using thermodynamics.