This study investigated the conformational dynamics of the guanidine-IV riboswitch upon ligand binding using single-molecule fluorescence resonance energy transfer (smFRET). The key findings are:
The aptamer domain of the guanidine-IV riboswitch exhibits higher sensitivity to guanidine compared to the terminator and full-length constructs. Magnesium ions (Mg2+) and guanidine (Gua+) facilitate the formation of a kissing loop (KL) in the aptamer domain, significantly increasing the KL-formed conformation.
In contrast, the addition of Gua+ and Mg2+ only had a minimal effect on the formation of the KL-formed anti-terminator structure in the terminator/anti-terminator or full-length RNA.
By mimicking the transcriptional process using position-specific labeling of RNA (PLOR) and smFRET, the authors discovered a narrow Gua+-sensitive transcriptional window for the guanidine-IV riboswitch, with a dramatic structural switch observed during the extension from 87 to 88 nucleotides upon Gua+ addition.
The authors propose a folding model for the guanidine-IV riboswitch, where the competition between the P2 stem and the KL structure determines the proportions of the terminator and the anti-terminator conformations as transcription progresses.
Overall, the study provides valuable insights into the ligand-response mechanism of the guanidine-IV riboswitch, highlighting the crucial role of the aptamer domain in sensing and regulating gene expression.
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by Gao,L., Chen... at www.biorxiv.org 12-05-2023
https://www.biorxiv.org/content/10.1101/2023.12.05.570130v2Deeper Inquiries