Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex

RNA aptamers obtained from in vitro selection experiments provide unique insights into the structural properties and ligand recognition capabilities of RNA in general. In order to investigate the relationships between RNA sequence information content and structural complexity with ligand affinity and specificity, the Szostak group previously identified eleven different families of GTP-binding aptamers varying widely in their sequence conservation patterns as well as in their secondary structure complexity and topology. The class V GTP aptamer has a particularly high affinity for GTP. Here, we report the high-resolution X-ray crystal structure of this aptamer-GTP complex. Remarkably, GTP is found to be integrated into one layer of a two-layered G-quadruplex, thereby rationalizing the high ligand affinity and the observed specificity. The G-quadruplex is extended on one side by a noncanonical tetrad layer containing three non-G nucleotides and on the other side by a Watson-Crick base pair stacking on top of an unpaired adenine. Interestingly, the G-nucleotides forming the G-quadruplex originate from two asymmetric bulges separated by an 8 base pair A-form helix, resulting in a complex and previously unobserved G-quadruplex topology.