RNA Nanostructures

This volume presents a collection of computational and experimental protocols pertaining to the creation, characterization, and utilization of RNA nanostructures. The chapters in this book cover topics such as ion effects in RNA folding; design and crystallography of self-assembling RNA nanostructures; x-aptamer selection and validation; RNAi in HIV-infected cells; and preparation of a conditional RNA switch. 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 thorough, RNA Nanostructures: Methods and Protocols is a valuable resource for the design and production of RNA nanostructures. Researchers and scientists sharing these detailed protocols is important for sustained progress in the field.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains keynotes and implementation advice from the experts Includes supplementary material: sn.pub/extras Includes supplementary material: sn.pub/extras

Inhalt

A New Method to Predict Ion Effects in RNA Folding.- Computational Generation of RNA Nanorings.- Protocols for Molecular Dynamics Simulations of RNA Nanostructures.- Rolling Circle Transcription for the Self-Assembly of Multimeric RNAi Structures and its Applications in Nanomedicine.- Computational Prediction of the Immunomodulatory Potential of RNA Sequences.- Co-Transcriptional Production of Chemically Modified RNA Nanoparticles.- Supported Fluid Lipid Bilayer as a Scaffold to Direct Assembly of RNA Nanostructures.- Evaluation of Thermal Stability of RNA Nanoparticles by Temperature Gradient Gel Electrophoresis (TGGE) in Native Condition.- Design and Crystallography of Self-Assembling RNA Nanostructures.- X-Aptamer Selection and Validation.- Design and Preparation of Aptamer-siRNA Chimeras (AsiCs) for Targeted Cancer Therapy.- Cellular Delivery of siRNAs using Bolaamphiphiles.- Preparation and Optimization of Lipid-Like Nanoparticles for mRNA Delivery.- Chitosan Nanoparticles formiRNA Delivery.- Synthesis of PLGA/Lipid Hybrid Nanoparticles for siRNA Delivery using the Emulsion Method PLGA-PEG/Lipid Nanoparticles for siRNA Delivery.- Oxime Ether Lipids as Transfection Agents: Assembly and Complexation with siRNA.- Polycationic Probe-Guided Nanopore Single-Molecule Counter for Selective miRNA Detection.- Intracellular Re-Association of RNA-DNA Hybrids that Activates RNAi in HIV-Infected Cells.- Construction and In Vivo Testing of Prokaryotic Riboregulators.- Preparation of a Conditional RNA Switch.- Rational Engineering of a Modular Group I Ribozyme to Control its Activity by Self-Dimerization.- CRISPR-Cas RNA Scaffolds for Transcriptional Programming in Yeast.- Using Planar Phi29 pRNA Three-Way Junction to Control Size and Shape of RNA Nanoparticles for Biodistribution Profiling in Mice. <p