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.

Keywords

• base mismatch
• RNA methylation
• RNA stability
• hydration, X-ray crystallography