A common RNA loop motif as a docking module and its function in the hammerhead ribozyme

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Abstract
Here I present a three-dimensional model of a novel element of RNA tertiary structure. A common loop motif composed of adjacent, sheared G.A and A.N non-canonical base pairs is proposed to form long-range tertiary interactions with other RNA residues. The widespread distribution of this G.A/A.N docking module suggests that the putative long-range docking interaction plays an important role in specifying the tertiary structure of large RNAs, and perhaps the quaternary structure of some intermolecular RNA-RNA interactions. Application of this docking module hypothesis to the hammerhead ribozyme provides crucial constraints for the calculation of three-dimensional models of its self-cleaving conformation.