Cooperative binding of bivalent ligands yields new insights into the guanidine-II riboswitch

1H, 13C, 15N and 31P chemical shift assignment of the first stem-loop Guanidine-II riboswitch from Escherichia coli

A comprehensive understanding of RNA-based gene regulation is a fundamental aspect for the development of innovative therapeutic options in medicine and for a more targeted response to environmental problems. Within the different mechanisms of RNA-based gene regulation, riboswitches are particularly interesting as they change their structure in response to the interaction with a low molecular weight ligand, often a well-known metabolite. Four distinct classes of riboswitches recognize the very small guanidinium cation. We are focused on the Guanidine-II riboswitch with the mini-ykkC motif. We report here the assignment of the 1H, 13C, 15N and 31P chemical shifts of the 23 nucleotide-long sequence of the first stem-loop of the Guanidine-II riboswitch aptamer from Escherichia coli. Despite its small size, the assignment of the NMR signals of this RNA proved to be challenging as it has symmetrical base pairs and palindromic character.