A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson–Crick base pairing

A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson–Crick base pairing

Melvin Calvin Building, Structural Biology Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720

Abstract

The crystal structure of the RNA dodecamer 5′-GGCC(GAAA)GGCC-3′ has been determined from x-ray diffraction data to 2.3-Å resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson–Crick base pairs make up an internal loop in the middle of the duplex, including sheared G·A pairs and novel asymmetric A·A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34° from end to end and the diameter is narrowed by 24% in the internal loop. A Mn²⁺ ion is bound directly to the N7 of the first guanine in the Watson–Crick region following the internal loop and the phosphate of the preceding residue. This Mn²⁺ location corresponds to a metal binding site observed in the hammerhead catalytic RNA.

Footnotes

↵ † Present address: Laboratory of Analytical Chemistry and Medicinal Physicochemistry, KULeuven, Edward Van Evenstraat 4, B-3000, Leuven, Belgium.
↵ ‡ Present address: Department of Chemistry and Biochemistry, Box 215, University of Colorado, Boulder, CO 80309.
Sung-Hou Kim, University of California, Berkeley, CA
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973 (reference 283D). The refined coordinates of the GAAA duplex have been deposited in the Nucleic Acids Database (NDB) (8) (URL051).