Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs

RNA. 2008 Oct;14(10):2125-35. doi: 10.1261/rna.1078508. Epub 2008 Sep 4.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adenine / chemistry*
  • Base Pair Mismatch*
  • Base Pairing
  • Crystallography, X-Ray
  • Guanosine / analogs & derivatives*
  • Guanosine / chemistry
  • Hydrogen Bonding
  • Methylation
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / radiation effects
  • RNA Stability* / radiation effects
  • Transition Temperature
  • Ultraviolet Rays

Substances

  • Guanosine
  • N(2),N(2)-dimethylguanosine
  • RNA
  • Adenine

Associated data

  • PDB/3CJZ