Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion

We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A stacking column at the minor groove side and two G bases are highly inclined, thereby forming the pocket-shaped motif at the major groove side. In the present structure, a hydrated Sr²⁺ ion exists in the pocket and binds to the O6 and N7 atoms of the two G bases and four phosphate groups. According to the previously-reported metal-binding properties to RNA molecules, many of divalent cations, such as Mg²⁺, Mn²⁺, Co²⁺, Zn²⁺, Ba²⁺, Pb²⁺ and Cd²⁺, may bind to the motif. This metal-binding motif can be used as a modular building block that allows for precise positioning of a single metal ion in functional nucleic acid molecules.