Structure of a Mispaired RNA Double Helix at 1.6-Å Resolution and Implications for the Prediction of RNA Secondary Structure

• Published in: Proceedings of the National Academy of Sciences - PNAS 1994-05, Vol.91 (10), p.4160-4164
• Main Authors: William B. T. Cruse, Saludjian, Pedro, Biala, Ewa, Strazewski, Peter, Prange, Thierry, Kennard, Olga
• Format: Article
• Language: English
• Subjects: Atoms; Base Composition; Biochemistry; Bromodeoxyuridine; Crystal structure; Crystallography; Crystallography, X-Ray - methods; Crystals; DNA; Electron density; Hydrogen Bonding; Hydrogen bonds; Models, Molecular; Molecules; Nucleic Acid Conformation; Oligodeoxyribonucleotides - chemistry; Pyrimidines; Ribonucleic acid; RNA; RNA - chemistry; Symmetry
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.91.10.4160

The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 Å, indicates an eight-base-pair A-RNA duplex containing a central block of two G·U and two C·U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-relatedBrU residues and are part of infinite double-helical stacks. The G·U pair is a wobble base pair analogous to the G·T pair found in DNA fragments. The C·U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. TheBrU·BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.