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Riboswitches as Targets and Tools
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1. Design of Transcription Regulating Riboswitches
Sven Findei, Manja Wachsmuth, Mario M¨orl, and PeterF. Stadler
2. Ligand-Dependent Exponential Amplification of Self-Replicating RNA Enzymes
Charles Olea, Jr. and Gerald F. Joyce
3. Design of Modular "Plug-and-Play Expression Platforms Derived From Natural Riboswitches for Engineering Novel Genetically Encodable RNA Regulatory Devices
Jeremiah J. Trausch and Robert Batey
4. Integrating and Amplifying Signal from Riboswitch Biosensors
Michael S. Goodson, Svetlana V. Harbaugh, Yaroslav G. Chushak and Nancy Kelley-Loughnane
5. Simple identification of two causes of noise in an aptazyme system by monitoring cell-free transcription.
Norikazu Ichihashi, Shungo Kobori, Tetsuya Yomo
6. Engineering of ribosomal shunt-modulating eukaryotic ON riboswitches by using a cell-free translation system
Atsushi Ogawa
7. Chemo-enzymatic Synthesis of Selectively 13C/15N-labeled RNA for NMR Structural and Dynamics Studies
Luigi J. Alvarado, Andrew P. Longhini, Regan LeBlanc, Bin Chen, Christoph Kreutz and T. Kwaku Dayie
8. In Vitro Analysis of Riboswitch-Spinach Aptamer Fusions as Metabolite-Sensing Fluorescent Biosensors
Colleen A. Kellenberger and Ming C. Hammond
9. Assaying Break and Nick-Induced Homologous Recombination in Mammalian Cells Using the DR-GFP Reporter and Cas9 Nucleases.
Lianne E.M. Vriend , Maria Jasin and Przemek M. Krawczyk
10. Adapting CRISPR/Cas9 for Functional Genomics Screens
Abba Malina , Alexandra Katigbak , Regina Cencic , Rayelle Itoua Maïga , Francis Robert, Hisashi Miura and Jerry Pelletier
11. The Icrispr Platform for Rapid Genome Editing in Human Pluripotent Stem Cells
Zengrong Zhu, Federico González and Danwei Huangfu
12. Using Riboswitches to Regulate Gene Expression and Define Gene Function in Mycobacteria
Erik Van Vlack and Jessica C. Seeliger
13. Controlling Expression of Genes in the Unicellular Alga Chlamydomonas Reinhardtii With a Vitamin-Repressible Riboswitch
Silvia Ramundo and Jean-David Rochaix
14. Conditional Control of Gene Expression by Synthetic Riboswitches in Streptomyces Coelicolor
Martin M. Rudolph, Michael-Paul Vockenhuber und Beatrix Suess
15. Engineering of Ribozyme-Based Aminoglycoside Switches of Gene Expression by in Vivo Genetic Selection in Saccharomyces Cerevisiae
Benedikt Klauser, Charlotte Rehm and Jörg S. Hartig
16. Kinetic Folding Design of Aptazyme-Regulated Expression Devices (aREDs) as Riboswitches for Metabolic Engineering
David Sparkman-Yager, Rodrigo A Correa-Rojas and James M Carothers
17. Riboselector: Riboswitch-Based Synthetic Selection Device to Expedite Evolution of Metabolite-Producing Microorganisms
Sungho Jang, Jina Yang, Sang Woo Seo and Gyoo Yeol Jung
18. Fluorescence Assays for Monitoring RNA-Ligand Interactions and Riboswitch-Targeted Drug Discovery Screening
J. Liu, C. Zeng, S. Zhou, J.A. Means and J.V. Hines
19. Monitoring Ribosomal Frameshifting as a Platform to Screen Anti-Riboswitch Drug Candidates
Chien-Hung Yu and René C. L. Olsthoorn
Sven Findei, Manja Wachsmuth, Mario M¨orl, and PeterF. Stadler
2. Ligand-Dependent Exponential Amplification of Self-Replicating RNA Enzymes
Charles Olea, Jr. and Gerald F. Joyce
3. Design of Modular "Plug-and-Play Expression Platforms Derived From Natural Riboswitches for Engineering Novel Genetically Encodable RNA Regulatory Devices
Jeremiah J. Trausch and Robert Batey
4. Integrating and Amplifying Signal from Riboswitch Biosensors
Michael S. Goodson, Svetlana V. Harbaugh, Yaroslav G. Chushak and Nancy Kelley-Loughnane
5. Simple identification of two causes of noise in an aptazyme system by monitoring cell-free transcription.
Norikazu Ichihashi, Shungo Kobori, Tetsuya Yomo
6. Engineering of ribosomal shunt-modulating eukaryotic ON riboswitches by using a cell-free translation system
Atsushi Ogawa
7. Chemo-enzymatic Synthesis of Selectively 13C/15N-labeled RNA for NMR Structural and Dynamics Studies
Luigi J. Alvarado, Andrew P. Longhini, Regan LeBlanc, Bin Chen, Christoph Kreutz and T. Kwaku Dayie
8. In Vitro Analysis of Riboswitch-Spinach Aptamer Fusions as Metabolite-Sensing Fluorescent Biosensors
Colleen A. Kellenberger and Ming C. Hammond
9. Assaying Break and Nick-Induced Homologous Recombination in Mammalian Cells Using the DR-GFP Reporter and Cas9 Nucleases.
Lianne E.M. Vriend , Maria Jasin and Przemek M. Krawczyk
10. Adapting CRISPR/Cas9 for Functional Genomics Screens
Abba Malina , Alexandra Katigbak , Regina Cencic , Rayelle Itoua Maïga , Francis Robert, Hisashi Miura and Jerry Pelletier
11. The Icrispr Platform for Rapid Genome Editing in Human Pluripotent Stem Cells
Zengrong Zhu, Federico González and Danwei Huangfu
12. Using Riboswitches to Regulate Gene Expression and Define Gene Function in Mycobacteria
Erik Van Vlack and Jessica C. Seeliger
13. Controlling Expression of Genes in the Unicellular Alga Chlamydomonas Reinhardtii With a Vitamin-Repressible Riboswitch
Silvia Ramundo and Jean-David Rochaix
14. Conditional Control of Gene Expression by Synthetic Riboswitches in Streptomyces Coelicolor
Martin M. Rudolph, Michael-Paul Vockenhuber und Beatrix Suess
15. Engineering of Ribozyme-Based Aminoglycoside Switches of Gene Expression by in Vivo Genetic Selection in Saccharomyces Cerevisiae
Benedikt Klauser, Charlotte Rehm and Jörg S. Hartig
16. Kinetic Folding Design of Aptazyme-Regulated Expression Devices (aREDs) as Riboswitches for Metabolic Engineering
David Sparkman-Yager, Rodrigo A Correa-Rojas and James M Carothers
17. Riboselector: Riboswitch-Based Synthetic Selection Device to Expedite Evolution of Metabolite-Producing Microorganisms
Sungho Jang, Jina Yang, Sang Woo Seo and Gyoo Yeol Jung
18. Fluorescence Assays for Monitoring RNA-Ligand Interactions and Riboswitch-Targeted Drug Discovery Screening
J. Liu, C. Zeng, S. Zhou, J.A. Means and J.V. Hines
19. Monitoring Ribosomal Frameshifting as a Platform to Screen Anti-Riboswitch Drug Candidates
Chien-Hung Yu and René C. L. Olsthoorn
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in riboswitches as targets and tools and contains sections on such topics as constructing and optimizing artificial riboswitches, live cell imaging and intracellular sensors with artificial riboswitches, conditional control of gene expression with artificial riboswitches, using artificial riboswitches for protein evolution and pathway optimization, and anti-riboswitch drug screens.