RNA folding and catalysis mediated by iron (II)

PLoS One. 2012;7(5):e38024. doi: 10.1371/journal.pone.0038024. Epub 2012 May 31.

Abstract

Mg²⁺ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg²⁺ in RNA folding and function can indeed be served by Fe²⁺. The results of quantum mechanical calculations show that the geometry of coordination of Fe²⁺ by RNA phosphates is similar to that of Mg²⁺. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4-P6 domain RNA is conserved between complexes with Fe²⁺ or Mg²⁺. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg²⁺, and the hammerhead ribozyme are enhanced in the presence of Fe²⁺ compared to Mg²⁺. All chemical footprinting and ribozyme assays in the presence of Fe²⁺ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe²⁺. The combined biochemical and paleogeological data are consistent with a role for Fe²⁺ in an RNA World. RNA and Fe²⁺ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg²⁺ alone.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalysis
  • Iron / metabolism*
  • Magnesium / metabolism
  • Nucleic Acid Conformation
  • RNA / chemistry
  • RNA / genetics
  • RNA Folding / genetics
  • RNA, Catalytic / genetics
  • Tetrahymena thermophila / genetics

Substances

  • RNA, Catalytic
  • hammerhead ribozyme
  • RNA
  • Iron
  • Magnesium