Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA -- RNA Footprinting Using Small Chemical Reagents -- Improving RNA Crystal Diffraction Quality by Post-Crystallization Treatment -- Using tRNA Scaffold to Assist RNA Crystallization -- RNA Modeling with the Computational Energy Landscape Framework -- Co-Expression and Co-Purification of RNA-Protein Complexes in Escherichia coli -- In Vivo Production of Small Recombinant RNAs Embedded in 5S rRNA-Derived Protective Scaffold -- Production of Circular Recombinant RNA in Escherichia coli Using Viroid Scaffolds -- Identification of RNA-Binding Proteins Associated to RNA Structural Elements -- Live Cell Imaging Using Riboswitch-Spinach tRNA Fusions as Metabolite-Sensing Fluorescent Biosensors -- Rational Design of Allosteric Fluorogenic RNA Sensors for Cellular Imaging -- Riboswitch-Mediated Detection of Metabolite Fluctuations During Live Cell Imaging of Bacteria -- FRET-Analysis of RNA-Protein-Interactions using Spinach-Aptamers -- Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach -- Aptazyme-Based Riboswitches and Logic Gates in Mammalian Cells -- Folding RNA-Protein Complex into Designed Nanostructures -- An Effective Method for Specific Gene Silencing in Escherichia coli Using Artificial Small RNA -- Expression and Purification of tRNA/pre-miRNA-Based Recombinant Noncoding RNAs -- Synthetic Biology Medicine and Bacteria-Based Cancer Therapeutics.

This second edition volume expands on the previous edition with discussions of recently developed techniques that use RNA scaffolds as molecular tools. These latest methods are used in the fields of molecular biology, cellular biology, nanotechnology, and structural biology. The chapters in this book cover topics such as RNA footprinting using small chemical reagents; using tRNA scaffolds to assist RNA crystallization; identification of RNA-binding proteins associated to RNA structural elements; and synthetic biology medicine and bacteria-based cancer therapeutics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, RNA Scaffolds: Methods and Protocols, Second Edition is a valuable resource that explores the fascinating uses of RNA in these different areas, and will inspire experts and novice researchers to further study this developing field. .