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NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs.

Tolbert BS, Kennedy SD, Schroeder SJ, Krugh TR, Turner DH

Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.

The NMR structures of [formula: see text] and [formula: see text] are reported. The internal loop, [formula: see text], is about 2 kcal/mol more stable than [formula: see text] at 37 degrees C. The duplexes assemble into similar global folds characterized by the formation of tandem sheared GA pairs. The different stabilities of the loops are accompained by differences in the local structure of the closing GU pairs. In the [formula: see text] internal loop, the GU pairs form canonical wobble configurations with two hydrogen bonds, whereas in [formula: see text], the GU pairs form a single hydrogen bond involving the amino group, GH22, and the carbonyl group, UO4. This pairing is similar to the GU closing pair of the 690 hairpin loop found in E. coli 16S rRNA. The [formula: see text] and [formula: see text] structures reveal how the subtle interplay between stacking and hydrogen bonding determines sequence dependent conformation and thermodynamic stability. Thus, this work provides structural and thermodynamic benchmarks for theoreticians in the ongoing effort to understand the sequence dependence of RNA physicochemical properties.

Published 7 February 2007 in Biochemistry, 46(6): 1511-22.
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