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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RNA Footprinting Using Small Chemical Reagents, differences that are known as the ligand “footprint.” Such footprints allow for the identification of the precise site of the ligand interaction, but also reveals RNA structural rearrangement upon ligand binding. Here we provide an experimental and analytical workflow to carry RNA footprinting experiments.

micronized

Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA,computational studies for RNA structures, at both the two-dimensional and the three-dimensional levels, led to several highly promising new developments. In this chapter, we describe a hybrid method, which combines the motif template-based Vfold3D model and the loop template-based VfoldLA model, to

Admonish

RNA Footprinting Using Small Chemical Reagents,onal structures that may form specific binding sites not only for proteins but for all sorts of molecules. Since the early days of molecular biology, strategies to probe RNA structure have been developed. Such probes are small molecules or RNases that most of the time specifically react with single

山顶可休息

Improving RNA Crystal Diffraction Quality by Postcrystallization Treatment,d viral RNAs. Here, we describe a protocol that combines postcrystallization dehydration and ion replacement that dramatically improved the diffraction quality of crystals of a large gene-regulatory tRNA–mRNA complex. Through this method, the resolution limit of X-ray data extended from 8.5 to 3.2 Å

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RNA Modeling with the Computational Energy Landscape Framework,of RNA molecules at an atomic level of detail. As RNA molecules are known to adopt multiple conformations with comparable energies, but different two-dimensional structures, all-atom models are necessary to better describe the structural ensembles for RNA molecules. This point is important because d

Cacophonous

,Coexpression and Copurification of RNA–Protein Complexes in , that allows for efficient in vivo expression of recombinant RNA in .. We have extended the “tRNA scaffold” method to RNA–protein coexpression in order to express and purify RNA by affinity in native condition. As a proof of concept, we present the expression and the purification of the AtRNA-mala i

Implicit

In Vivo Production of Small Recombinant RNAs Embedded in 5S rRNA-Derived Protective Scaffold,itro. Herein, we describe an alternative approach in which RNAs of interest are expressed as a fusion with a 5S rRNA-derived scaffold. The scaffold provides protection against cellular ribonucleases resulting in cellular accumulations comparable to those of regular ribosomal RNAs. After isolation of

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Production of Circular Recombinant RNA in , Using Viroid Scaffolds,ery stable scaffolds to produce recombinant RNA in .. Coexpression of an RNA precursor consisting of a viroid monomer, in which the RNA of interest is inserted, flanked by domains of the viroid hammerhead ribozyme, along with a host plant tRNA ligase, the enzyme that catalyzes viroid circularization