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Chemical substitution: On early Earth, iron may have performed magnesium’s #RNA folding job:… #scidaily @MyEN
RNA Folding and Catalysis Mediated by Iron (II)
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 P4P6 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.
RNA can bind and sense the shapes of other molecules by feeling them with its backbone—and not just its bases. What gives RNA molecules this remarkable versatility?
By Anna Marie Pyle
What pulls catalytic RNA together
Group II introns have a conserved secondary structure consisting of six domains (magenta) that are flanked by the upstream and downstream exons (orange). In the first step of splicing (1), a bulged adenosine in domain 6 (DVI) attacks the phosphate at the 5′-splice site, becoming covalently attached to it and releasing the 5′-exon. In the second step of splicing (2), the 5′ terminus attacks the phosphate at the 3′-splice site, thereby joining the two exons (splicing them together) and releasing the lariat-shaped group II intron. The group II intron’s crystal structure is shown above, with the catalytically important domain V (DV) marked in magenta.