Effects of N 2 ,N 2 -dimethylguanosine on RNA structure and stability: Crystal structure of an RNA duplex with tandem m 2 2 G:A pairs

• Published in: RNA (Cambridge) Vol. 14; no. 10; pp. 2125 - 2135
• Main Authors: Pallan, Pradeep S., Kreutz, Christoph, Bosio, Silvia, Micura, Ronald, Egli, Martin
• Format: Journal Article
• Language: English
• Published: 01.10.2008
• ISSN: 1355-8382; 1469-9001
• DOI: 10.1261/rna.1078508

Methylation of the exocyclic amino group of guanine is a relatively common modification in rRNA and tRNA. Single methylation ( N 2 -methylguanosine, m 2 G) is the second most frequently encountered nucleoside analog in Escherichia coli rRNAs. The most prominent case of dual methylation ( N 2 ,N 2 -dimethylguanosine, m 2 2 G) is found in the majority of eukaryotic tRNAs at base pair m 2 2 G26:A44. The latter modification eliminates the ability of the N 2 function to donate in hydrogen bonds and alters its pairing behavior, notably vis-à-vis C. Perhaps a less obvious consequence of the N 2 ,N 2 -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 m 2 2 G: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 N 2 -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.