The role of specific 2′-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA

Abstract

The role of 2′-hydroxyl groups in stabilizing the tightly kinked geometry of the kink-turn (K-turn) has been investigated. Individual 2′-OH groups have been removed by chemical synthesis, and the kinking of the RNA has been studied by gel electrophoresis and fluorescence resonance energy transfer. The results have been analyzed by reference to a database of 11 different crystallographic structures of K-turns. The potential hydrogen bonds fall into several classes. The most important are those in the core of the turn and ribose-phosphate interactions around the bulge. Of these the single most important hydrogen bond is one donated from the 2′-OH of the 5′ nucleotide of the bulge to the N1 of the adenine of the kink-proximal A•G pair. This is present in all known K-turn structures, and removal of the 2′-OH completely prevents metal ion-induced folding. Hydrogen bonds formed in the minor grooves of the helical stems are less important, and removal of the participating 2′-OH groups leads to reduced impairment of folding. These interactions are generally more polymorphic, and hydrogen bonds probably form where possible, as permitted by the global structure. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 RNA Society.