Effects of N2,N2 -dimethylguanosine on RNA structure and stability: Crystal structure of an RNA duplex with tandem m22G:A pairs
Abstract
Methylation of the exocyclic amino group of guanine is a relatively common modification in rRNA and tRNA. Single methylation (N2 -methylguanosine, m2G) is the second most frequently encountered nucleoside analog in Escherichia coli rRNAs. The most prominent case of dual methylation (N2,N2 -dimethylguanosine, m2 2G) is found in the majority of eukaryotic tRNAs at base pair m2 2G26:A44. The latter modification eliminates the ability of the N2 function to donate in hydrogen bonds and alters its pairing behavior, notably vis-à-vis C. Perhaps a less obvious consequence of the N2,N2 -dimethyl modification is its role in controlling the pairing modes between G and A. We have determined the crystal structure of a 13-mer RNA duplex with central tandem m2 2G:A pairs. In the structure both pairs adopt an imino-hydrogen bonded, pseudo-Watson–Crick conformation. Thus, the sheared conformation frequently seen in tandem G:A pairs is avoided due to a potential steric clash between an N2 -methyl group and the major groove edge of A. Additionally, for a series of G:A containing self-complementary RNAs we investigated how methylation affects competitive hairpin versus duplex formation based on UV melting profile analysis.
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Reprint requests to: Martin Egli, Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA; e-mail: martin.egli{at}vanderbilt.edu; fax: (615) 322-7122; or Ronald Micura, Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Innsbruck University, 6020 Innsbruck, Austria; e-mail: ronald.micura{at}uibk.ac.at; fax: +43-512-507-2892.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.1078508.
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- Received March 14, 2008.
- Accepted July 10, 2008.
- Copyright © 2008 RNA Society
