Conformation and mechanical property of rpoS mRNA inhibitory stem studied by optical tweezers and X-ray scattering

Autoři: Xinyao Hu aff001;  Xuanling Li aff001;  Lingna Yang aff002;  Yilin Zhu aff001;  Yunyu Shi aff001;  Yinmei Li aff001;  Haowei Wang aff001;  Qingguo Gong aff001
Působiště autorů: Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China aff001;  School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China aff002
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0222938


3′ downstream inhibitory stem plays a crucial role in locking rpoS mRNA 5' untranslated region in a self-inhibitory state. Here, we used optical tweezers to study the unfolding/refolding of rpoS inhibitory stem in the absence and presence of Mg2+. We found adding Mg2+ decreased the free energy of the RNA junction without re-arranging its secondary structure, through confirming that this RNA formed a canonical RNA three-way junction. We suspected increased free energy might change the relative orientation of different stems of rpoS and confirmed this by small angle X-ray scattering. Such changed conformation may improve Hfq-bridged annealing between sRNA and rpoS RNA inhibitory stem. We established a convenient route to analyze the changes of RNA conformation and folding dynamics by combining optical tweezers with X-ray scattering methods. This route can be easily applied in the studies of other RNA structure and ligand-RNA.

Klíčová slova:

DNA transcription – Free energy – RNA structure – RNA annealing – Small-angle scattering – Molecular structure – Magnesium chloride – RNA folding


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2019 Číslo 9