Discovery of TPP derivatives binding to riboswitch and structural dynamics studies using NMR spectroscopy

Abstract

RNAs usually respond to environmental factors and regulate their chemical changes. Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism. We studied about development of TPP analogues that replace 4-aminopyrimidine group and thiazole ring of TPP to 7-azaindole group and to trizole, respectively. The interactions between the riboswitch and the synthesized analogues weren’t identified, but the structural characteristics of the analogues for interaction were revealed.