Main description:

This volume provides techniques on recent developments that use RNA scaffolds as molecular tools. RNA Scaffolds: Methods and Protocols guides readers through methods on various domains as molecular biology, nanotechnologies, and structural biology. Written for the Methods in Molecular Biology series, 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.Practical and authoritative, RNA Scaffolds: Methods and Protocols will serve as an invaluable reference for those interested in further study into this fascinating field.

Contents:

1. A Method to Predict the 3D Structure of an RNA Scaffold

Xiaojun Xu and Shi-Jie Chen

2. Post-crystallization Improvement of RNA Crystal Diffraction Quality

Jinwei Zhang and Adrian R. Ferre-D'Amare

3. Expression and Purification of RNA-protein Complexes in Escherichia coli

El Khouri M, Catala M, Seijo B, Chabal J, Tisne C, Dardel F, and Ponchon L

4. Production of Homogeneous Recombinant RNA using a tRNA Scaffold and Hammerhead Ribozymes

Frank H.T. Nelissen, Hans A. Heus, and Sybren S. Wijmenga

5. In vivo Production of Small Recombinant RNAs Embedded in 5S rRNA-Derived Protective Scaffold

Victor G. Stepanov and George E. Fox

6. Detection of RNA-Protein Interactions using Tethered RNA Affinity Capture

IIOKA H. and Macara I.G.

7. A Universal Method for Labeling Native RNA in Live Bacterial Cells

Irina Smolina and Natalia Broude

8. Live Cell Imaging Using Riboswitch-Spinach tRNA Fusions as Metabolite-Sensing Fluorescent Biosensors

Colleen A. Kellenberger, Zachary F. Hallberg, and Ming C. Hammond

9. RNA Scaffold: Designed To Co-Localize Enzymes

ZJU_China team and Ming Chen

10. Artificial Ligase Ribozymes Isolated by a "Design And Selection" Strategy

Shigeyoshi Matsumura and Yoshiya Ikawa

11. Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach

Charlotte Rehm, Benedikt Klauser, and Joerg S. Hartig

12. Aptazyme-Based Riboswitches and Logic Gates in Mammalian Cells

Yoko Nomura and Yohei Yokobayashi

13. Design and Characterisation of Topological Small RNAs

Jack Hassall, Paul MacDonald, Teresa Cordero, William Rostain, and Alfonso Jaramillo

14. Folding RNA-Protein Complex into Designed Nanostructures

Tomonori Shibata, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, and Hirohide Saito

15. Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60 to 90 or 108

Emil F. Khisamutdinov, My Nguyen Hoan Bui, Daniel Jasinski, Zhengyi Zhao, Zheng Cui, and Peixuan Guo

16. RNA-Mediated CdS Based Nanostructures

Vinit Kumar and Anil Kumar

17. An Effective Method for Specific Gene Silencing in Escherichia coli using Artificial Small RNA

Geunu Bak, Jee Soo Choi, Wonkyeong Kim, Shinae Suk, and Younghoon Lee