Summary information and primary citation

PDB-id
6hbx; DSSR-derived features in text and JSON formats
Class
RNA
Method
X-ray (1.54 Å)
Summary
The structure of the g. violaceus guanidine ii riboswitch p2 stem-loop with ethylguanidine
Reference
Huang L, Wang J, Wilson TJ, Lilley DMJ (2019): "Structure-guided design of a high-affinity ligand for a riboswitch." Rna, 25, 423-430. doi: 10.1261/rna.069567.118.
Abstract
We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by Cn linkers where n = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a ten-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands have potential applications in chemical biology.

Cartoon-block schematics in six views (download the tarball)

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