SOME FUNCTIONAL INSIGHTS FROM RNA CRYSTAL STRUCTURES. Martin Egli, Dept. of Mol. Pharm. & Biol. Chem., Northwestern University Medical School, 303 East Chicago Ave., Chicago, IL 60611-3008, USA

The conformational features of an RNA A-form duplex with single adenosine bulges in two crystal structures will be discussed. Bulged nucleotides are frequent secondary structure motifs in RNA molecules and are often involved in RNA-RNA and RNA-protein interactions. RNA can be efficiently and selectively cleaved at bulge sites in the presence of divalent metal cations. The bulged As are looped-out, kink the duplex into the minor groove, and cause a marked opening of the normally cavernous RNA major groove. The distinct geometries around the A-bulges in the two structures indicate that bulges can confer considerable local plasticity on the usually rigid RNA double helix. The enhanced backbone flexibility can provide for a linear preorientation of the attacking 2'-oxygen of the bulge nucleotide and the P-O5' bond of the adjacent phosphate, consistent with RNA self-cleavage at bulged sites.

The crystal structure of the RNA duplex [r(CCCCGGGG)]₂ was refined to 1.45 Å resolution using room temperature synchrotron diffraction data. This represents the highest resolution reported to date for an all-RNA oligonucleotide. Analysis of the ordered hydration around the octamer duplex reveals conserved regular arrangements of water molecules in both grooves. Evidence will be provided for an important role of the 2'-hydroxyl groups in the thermodynamic stabilization of RNA relative to DNA beyond their known functions of locking the sugar pucker and mediating 3'->5' intra-strand O2'...O4' hydrogen bonds.