Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement

Bulges are common structural motifs in RNA secondary structure and are thou ght to play important roles in RNA-protein and RNA-drug interactions. Adeno sine bases are the most commonly occurring unpaired base in double helical RNA secondary structures. The solution conformation and dynamics of a 25-nu cleotide RNA duplex containing an unpaired adenosine, r(GGCAGAGUGCCGC): r(G CGGCACCUGCC) have been studied by NMR spectroscopy and MORASS iterative rel axation matrix structural refinement. The results show that the bulged aden osine residue stacks into the RNA duplex with little perturbation around th e bulged region. Most of the bases in the RNA duplex adopt C-3'-endo confor mation, exhibiting the N-type sugar pucker as found in the A form helices. The sugars of the bulged residue and the 5' flanking residue to it are foun d to exhibit C-2'-endo conformation. None of the residues are in syn confor mation. (C) 2000 Academic Press.