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Article

NMR Structures of (rGCUGAGGCU)₂ and (rGCGGAUGCU)₂: Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs^†^,^‡

Supporting Info

Blanton S. Tolbert,^§ Scott D. Kennedy,^§ Susan J. Schroeder, Thomas R. Krugh, and Douglas H. Turner*^#

Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019-3051, Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, and Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642

Biochemistry, 2007, 46 (6), pp 1511–1522

DOI: 10.1021/bi061350m

Publication Date (Web): January 20, 2007

†

This work was supported by NIH Grant GM22939 (to D.H.T.). We also thank NIGMS for providing minority supplement grant GM22939 to B.S.T.

‡

The coordinates have been deposited as Protein Data Bank entries 2IRN and 2IRO.

Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry.

University of Oklahoma.

Department of Chemistry, University of Rochester.

Corresponding author. Phone: 585-275-3207. Fax: 585-276-0205. E-mail: turner@chem.rochester.edu.

Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester School of Medicine and Dentistry.

Abstract

The NMR structures of and are reported. The internal loop, , is about 2 kcal/mol more stable than at 37 °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 internal loop, the GU pairs form canonical wobble configurations with two hydrogen bonds, whereas in , 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 and 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.