Titlebook: RNA Scaffolds; Methods and Protocol Luc Ponchon Book 2021Latest edition Springer Science+Business Media, LLC, part of Springer Nature 2021

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万神殿

Riboswitch-Mediated Detection of Metabolite Fluctuations During Live Cell Imaging of Bacteria,the riboswitch. This method describes how reporters for live cell imaging, such as yellow fluorescent protein (YFP), can be placed under genetic control by metabolite-sensing riboswitches in the bacterium .. Specifically, a protocol for generating a fluorescent YFP reporter, based on a c-di-GMP responsive riboswitch, is outlined below.

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Improving RNA Crystal Diffraction Quality by Postcrystallization Treatment,, enabling structure determination. Although this protocol was developed for a particular RNA complex, the general importance of solvent and counterions in nucleic acid structure may render it generally useful for crystallographic analysis of other RNAs.

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In Vivo Production of Small Recombinant RNAs Embedded in 5S rRNA-Derived Protective Scaffold, the chimeric RNA from the cells, the scaffold can be removed, if necessary, by deoxyribozyme-catalyzed cleavage followed by preparative electrophoretic separation of the reaction products. The protocol is designed for sustained production of high quality RNA on the milligram scale.

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Identification of RNA-Binding Proteins Associated to RNA Structural Elements,nalysis to identify novel interactors recognizing RNA structural domains. This approach takes advantage of tRNA-scaffold guided expression, allowing the identification of factors belonging to networks involved in RNA and protein metabolism.

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Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA,e assembly from templates of motifs and loops. For illustration, we use the ZIKV xrRNA1 as an example to show the template-based prediction of RNA 3D structures from the 2D structure. The web server for the hybrid model is freely accessible at ..