The 1.3 Å resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): Metal ion binding correlates with base unstacking and groove contraction

Abstract

Metal ions play a key role in RNA folding and activity. Elucidating the rules that govern the binding of metal ions is therefore an essential step for better understanding the RNA functions. High-resolution data are a prerequisite for a detailed structural analysis of ion binding on RNA and, in particular, the observation of monovalent cations. Here, the high-resolution crystal structures of the tridecamer duplex r(GCGUUUGAAACGC) crystallized under different conditions provides new structural insights on ion binding on GAAA/UUU sequences that exhibit both unusual structural and functional properties in RNA. The present study extends the repertory of RNA ion binding sites in showing that the two first bases of UUU triplets constitute a specific site for sodium ions. A striking asymmetric pattern of metal ion binding in the two equivalent halves of the palindromic sequence demonstrates that sequence and its environment act together to bind metal ions. A highly ionophilic half that binds six metal ions allows, for the first time, the observation of a disodium cluster in RNA. The comparison of the equivalent halves of the duplex provides experimental evidences that ion binding correlates with structural alterations and groove contraction.

Noncanonical G(syn)–G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex

“…The G(syn)-G(anti) base pair has been observed in RNA in only a few cases: in the 16S rRNA of the Escherichia coli ribosome (Schuwirth et al 2005), in the HIV Rev response element hairpin (Ippolito and Steitz 2000) and its duplex model (Hung et al 2000), and in synthetic RNA duplexes studied by X-ray (Timsit and Bombard 2007) and by NMR methods (Burkard and Turner 2000). Despite being embedded in different sequence and structural contexts, the above structures share similar G-G base-pair geometry, which includes G(carbonyl)-G(N1) and G(N7)-G(exoamino) hydrogen bonds.…”

Computational Exploration of Mobile Ion Distributions around RNA Duplex

“…For example the persistence length of RNA is of order of 500Å55 while the B-factors are especially small (about 8 per residue) 16.Our study focuses on the properties of the ions, their thermodynamic properties and their mobility near the polyelectrolyte. There is a vast number of studies that model the RNA as rigid and describe the properties of the ions by continuum theories.…”

Nucleobase carbonyl groups are poor Mg2+inner-sphere binders but excellent monovalent ion binders—a critical PDB survey

“…S8B) and a lysine riboswitch (resolution: 1.9 Å; Fig. 5B) were crystallized in buffers containing Mn 2+ and 100 mM NaCl or Mg 2+ , K + and 100 mM Na + citrate, respectively (Timsit and Bombard 2007;Serganov et al 2008). Out of a total of 29 Na + , the latter structure contains 17 hexacoordinated Na + with 10 displaying d(Na + …O) in the 2.3-2.6 Å range.…”