RNA Scaffolds: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

1. Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA
Xiaojun Xu and Shi-Jie Chen

2. RNA Footprinting Using Small Chemical Reagents
Gr嶲oire De Bisschop and Bruno Sargueil

3. Improving RNA Crystal Diffraction Quality by Post-Crystallization Treatment
Jinwei Zhang and Adrian R. Ferr?D'Amar?

4. Using tRNA Scaffold to Assist RNA Crystallization
Changrui Lu, Rujie Cai, Jason C. Grigg, and Ailong Ke

5. RNA Modeling with the Computational Energy Landscape Framework
Konstantin R鐰er and Samuela Pasquali

6. Co-Expression and Co-Purification of RNA-Protein Complexes in Escherichia coli
Margot El Khouri, Marjorie Catala, Bili Seijo, Johana Chabal, Fr嶮廨ic Dardel, Carine Tisn? and Luc Ponchon

7. In Vivo Production of Small Recombinant RNAs Embedded in 5S rRNA-Derived Protective Scaffold
Victor G. Stepanov and George E. Fox

8. Production of Circular Recombinant RNA in Escherichia coli Using Viroid Scaffolds
Jos?Antonio Dar瓋

9. Identification of RNA-Binding Proteins Associated to RNA Structural Elements
Javier Fernandez-Chamorro, Rosario Francisco-Velilla, Azman Embarc-Buh, and Encarnacion Martinez-Salas

10. Live Cell Imaging Using Riboswitch-Spinach tRNA Fusions as Metabolite-Sensing Fluorescent Biosensors
Sudeshna Manna, Colleen A. Kellenberger, Zachary F. Hallberg, and Ming C. Hammond

11. Rational Design of Allosteric Fluorogenic RNA Sensors for Cellular Imaging
Qikun Yu, Ru Zheng, Manojkumar Narayanan, and Mingxu You

12. Riboswitch-Mediated Detection of Metabolite Fluctuations During Live Cell Imaging of Bacteria
Cordelia A. Weiss and Wade C. Winkler

13. FRET-Analysis of RNA-Protein-Interactions using Spinach-Aptamers
Laura Roszyk and Sven Hennig

14. Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach
Charlotte Rehm, Benedikt Klauser, Monika Finke, and J顤g S. Hartig

15. Aptazyme-Based Riboswitches and Logic Gates in Mammalian Cells
Yoko Nomura and Yohei Yokobayashi

16. Folding RNA-Protein Complex into Designed Nanostructures
Tomonori Shibata, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, and Hirohide Saito

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

18. Expression and Purification of tRNA/pre-miRNA-Based Recombinant Noncoding RNAs
Mei-Juan Tu, Halley K. Wright, Neelu Batra, and Ai-Ming Yu

19. Synthetic Biology Medicine and Bacteria-Based Cancer Therapeutics
Jaehyung Lee, Andrew C. Keates, and Chiang J. Li

Subject Index List...