Ribozymes - Bog

Part I: Ribozyme Function
1. Conjugation as a Highly Sensitive Assay to Study Group II Intron Splicing in vivo
Félix LaRoche-Johnston, Caroline Monat, and Benoit Cousineau

2. Co-transcriptional Analysis of Self-cleaving Ribozymes and their Ligand Dependence
Luiz F. M. Passalacqua and Andrej Lupták

Part II: Ribozyme Indentification and Characterization
3. Cloning and Detection of Genomic Retrozymes and their circRNA Intermediates
Amelia Cervera and Marcos de la Pe├▒a

4. Demonstration of a Ribozyme in Epsilon Domain of Hepatitis B Virus RNA
Dibyajnan Chakraborty and Sagarmoy Ghosh

5. In vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-loop Substrate
Pierre Dagenais and Pascale Legault

6. Characterization and Optimization of a Deoxyribozyme with a Short Left Binding Arm
Yueyao Wang and Hanyang Yu

7. Computer-aided Design of Active Pseudoknotted Hammerhead Ribozymes
Sabrine Najeh, Kasra Zandi, Samia Djerroud, Nawwaf Kharma, and Jonathan Perreault

8. Inverse RNA Folding Workflow to Design and Test Ribozymes Including Pseudoknots
Mohammad Kayedkhordeh, Ryota Yamagami, Philip C. Bevilacqua, and David H. Mathews

Part III : Ribozyme Structure
9. Using an L7Ae-tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs
Stella M. Lai and Venkat Gopalan

10. SHAPE Profiling to Probe Group II Intron Conformational Dynamics during Splicing
Timothy Wiryaman and Navtej Toor
11. Dynamics-Function Analysis in Catalytic RNA Using NMR Spin Relaxation and Conformationally Restricted Nucleotides
Charles G. Hoogstraten, Montserrat Terrazas, Anna Avi├▒├│, Neil A. White, and Minako Sumita

Part IV : Ribozyme Conjugations
12. Design and Evaluation of Guide RNA Transcripts with a 3''-terminal HDV Ribozyme to Enhance CRISPR-based Gene Inactivation
Ben Berkhout, Zongliang Gao and Elena Herrera-Carrillo

13. Design and Evaluation of AgoshRNAs with 3''-terminal HDV Ribozymes to Enhance the Silencing Activity
Ben Berkhout and Elena Herrera-Carrillo

14. Cloning and Detection of Aptamer-ribozyme Conjugations
Ryan P. Goguen, Anne Gatignol, and Robert J. Scarborough

Part V: Ribozyme as Tools to Study other RNAs
15. Use of a Lariat Capping Ribozyme to Study Cap Function in Vivo
Max Pietschmann, Gregor Tempel, Maral Halladjian, Nicolai Krogh, and Henrik Nielsen

16. Long Non-coding RNA Depletion using Self-cleaving Ribozymes
Alex C Tuck and Marc B├╝hler