Bulged Adenosine Influence on the RNA Duplex Conformation in Solution

ABSTRACT : The RNA single bulge motif is an unpaired residue within a strand of several complementarybase pairs. To gain insight into structural changes induced by the presence of the adenosine bulge onRNA duplex, the solution structures of RNA duplex containing a single adenine bulge (5′-GCAGAA-GAGCG-3′/5′-CGCUCUCUGC-3′) and a reference duplex with all Watson-Crick base pairs (5′-GCAGAGAGCG-3′/5′-CGCUCUCUGC-3′) have been determined by NMR spectroscopy. The referenceduplex structure is a regular right-handed helix with all of the attributes of an A-type helix. In the bulgedduplex, single adenine bulge stacks into the helix, and the bulge region forms a well-defined structure.Both structures were analyzed by the use of calculated helical parameters. Distortions induced by theaccommodation of unpaired residue into the helical structure propagate over the entire structure and aremanifested as the reduced base pairs inclination and x-displacement. Intrahelical position of bulged adenineA5 is stabilized by efficient stacking with 5′-neighboring residues G4.RNA molecules form complex tertiary structures that areclosely related with their functions