Open AccessConformation and mechanical property of rpoS mRNA inhibitory stem studied by optical tweezers and X-ray scattering
Author(s) -
Xinyao Hu,
Xuanling Li,
Lingna Yang,
Yilin Zhu,
Yunyu Shi,
Yinmei Li,
Haowei Wang,
Qingguo Gong
Publication year - 2019
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0222938
Subject(s) - rna , optical tweezers , rpos , inhibitory postsynaptic potential , chemistry , biophysics , stem loop , messenger rna , scattering , crystallography , physics , biology , biochemistry , optics , gene , gene expression , promoter , neuroscience
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 Mg 2+ . We found adding Mg 2+ 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.