RNA Scaffolds

1. Front Matter

   Pages i-xiii

   PDF

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

   • Xiaojun Xu, Shi-Jie Chen

   Pages 1-11

3. Post-crystallization Improvement of RNA Crystal Diffraction Quality

   • Jinwei Zhang, Adrian R. Ferré-D’Amaré

   Pages 13-24

4. Expression and Purification of RNA–Protein Complexes in Escherichia coli

   • Margueritte El Khouri, Marjorie Catala, Bili Seijo, Johana Chabal, Carine Tisné, Frédéric Dardel et al.

   Pages 25-31

5. Production of Homogeneous Recombinant RNA Using a tRNA Scaffold and Hammerhead Ribozymes

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

   Pages 33-44

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

   • Victor G. Stepanov, George E. Fox

   Pages 45-65

7. Detection of RNA–Protein Interactions Using Tethered RNA Affinity Capture

   • Hidekazu Iioka, Ian G. Macara

   Pages 67-73

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

   • Irina Smolina, Natalia Broude

   Pages 75-85

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

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

   Pages 87-103

10. RNA Scaffold: Designed to Co-localize Enzymes

    • ZJU_China Team (iGEM 2012), Ming Chen

    Pages 105-112

11. Artificial Ligase Ribozymes Isolated by a “Design and Selection” Strategy

    • Shigeyoshi Matsumura, Yoshiya Ikawa

    Pages 113-125

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

    • Charlotte Rehm, Benedikt Klauser, Jörg S. Hartig

    Pages 127-140

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

    • Yoko Nomura, Yohei Yokobayashi

    Pages 141-148

14. Design and Characterization of Topological Small RNAs

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

    Pages 149-167

15. Folding RNA–Protein Complex into Designed Nanostructures

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

    Pages 169-179

16. 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, Peixuan Guo

    Pages 181-193

17. RNA-Mediated CdS-Based Nanostructures

    • Vinit Kumar, Anil Kumar

    Pages 195-210

18. An Effective Method for Specific Gene Silencing in Escherichia coli Using Artificial Small RNA

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

    Pages 211-225

19. Back Matter

    Pages 227-231

    PDF

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.

• DSL ribozyme
• RNA origami
• RNA protein co-production in the bacteria
• RNA structure data bank
• Vfold
• aptazymes
• data acquisition
• nano-objects
• potentialization of the silencing activity
• riboswitches

• University of Paris Descartes, Paris, France

  Luc Ponchon

Policies and ethics