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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 riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, and ligand interactions and thermodynamics. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in riboswitch discovery, structure and function - Contains sections on such topics as…mehr
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 riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, and ligand interactions and thermodynamics. - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in riboswitch discovery, structure and function - Contains sections on such topics as riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, ligand interactions and thermodynamics
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Inhaltsangabe
1. Riboswitch Discovery By Combining Rna-Seq And Genome-Wide Identification Of Transcriptional Start Sites Isabelle Rosinski-Chupin, Olga Soutourina and Isabelle Martin-Verstraete 2. Discovering Human RNA Aptamers by Structure-Based Bioinformatics and Genome-Based in Vitro Selection Bao Ho, Julio Polanco, Randi Jimenez, and Andrej Lupták 3. Affinity Purification of In Vitro Transcribed RNA with Homogeneous Ends Using a 3'-ARiBo Tag Geneviève Di Tomasso, Alix Salvail-Lacoste, Jonathan Bouvette, James G. Omichinski and Pascale Legault 4. Deoxyribozyme-mediated Ligation for Incorporating EPR Spin Labels and Reporter Groups into RNA Katarzyna Wawrzyniak-Turek and Claudia Höbartner 5. A Flexible, Scalable Method for Preparation of Homogeneous Aminoacylated tRNAs Jinwei Zhang and Adrian R. Ferré-D'Amaré 6. Synthesis of A Biotinylated Photocleavable Nucleotide Monophosphate for the Preparation of Natively Folded RNAs. Yiling Luo, Herman O Sintim and T. Kwaku Dayie 7. Chemo-Enzymatic Synthesis of Selectively 13c/15n-Labeled Rna for Nmr Structural and Dynamics Studiess T. Kwaku Dayie, Luigi J. Alvarado, Andrew P. Longhini, Regan LeBlanc, Bin Chen, Cristoph Kreutz, Luigi J. Alvarado, Andrew P. Longhini, Regan LeBlanc, Bin Chen and Christoph Kreutz 8. RNA SHAPE Analysis of Small RNAs and Riboswitches Greggory M. Rice, Steven Busan, Fethullah Karabiber, Oleg V. Favorov , and Kevin M. Weeks. 9. Experimental Approaches for Measuring pKa's in RNA and DNA Pallavi Thaplyal and Philip C. Bevilacqua 10. Crystallographic Analysis of Tpp Riboswitch Binding by Small Molecule Ligands Discovered Through Fragment-Based Drug Discovery Approaches Katherine Deigan Warner and Adrian R. Ferré-D'Amaré 11. Methods for using New Conceptual Tools and Parameters to Assess RNA Structure by Small-Angle X-ray Scattering Francis E. Reyes, Camille R. Schwartz, John A. Tainer and Robert P. Rambo 12. Use of 19F NMR Methods to Probe Conformational Heterogeneity and Dynamics of Exchange in Functional RNA Molecules Caijie Zhao and Nancy L. Greenbaum 13. Site-Directed Spin-Labeling Strategies and Electron Paramagnetic Resonance Spectroscopy for Large Riboswitches Jackie M. Esquiaqui, Eileen M. Sherman, Jing-Dong Ye, and Gail E. Fanucci 14. Using sm-FRET and Denaturants to Reveal Folding Landscapes Euan Shaw, Patrick St-Pierre, Kaley McCluskey, Daniel A. Lafontaine and J. Carlos Penedo 15. Riboswitch Structure and Dynamics by smFRET Microscopy Krishna C. Suddala and Nils G. Walter 16. Ribosome Structure and Dynamics by smFRET Microscopy Bassem Shebl, Zenia Norman and Peter V. Cornish 17. Unraveling the Thermodynamics and Kinetics of RNA Assembly: Surface Plasmon Resonance, Isothermal Titration Calorimetry, and Circular Dichroism Charles G. Hoogstraten, Minako Sumita and Neil A. White 18. ITC Analysis of Ligand Binding to PreQ1 Riboswitches Joseph A. Liberman, Jarrod T. Bogue, Jermaine L. Jenkins, Mohammad Salim , and Joseph E. Wedekind. 19. Facile Characterization of Aptamer Kinetic and Equilibrium Binding Properties using Surface Plasmon Resonance Andrew L. Chang, Maureen McKeague and Christina D. Smolke 20. The AdoCbl-riboswitch Interaction Investigated by In-line Probing and Surface Plasmon Resonance (SPR) Spectroscopy Michelle F. Schaffer, Pallavi K. Choudhary and Roland K. O. Sigel 21. Assessing RNA Interactions with Proteins by DRaCALA Darshan K. Patel, Margo P. Gebbie and Vincent T. Lee
1. Riboswitch Discovery By Combining Rna-Seq And Genome-Wide Identification Of Transcriptional Start Sites Isabelle Rosinski-Chupin, Olga Soutourina and Isabelle Martin-Verstraete 2. Discovering Human RNA Aptamers by Structure-Based Bioinformatics and Genome-Based in Vitro Selection Bao Ho, Julio Polanco, Randi Jimenez, and Andrej Lupták 3. Affinity Purification of In Vitro Transcribed RNA with Homogeneous Ends Using a 3'-ARiBo Tag Geneviève Di Tomasso, Alix Salvail-Lacoste, Jonathan Bouvette, James G. Omichinski and Pascale Legault 4. Deoxyribozyme-mediated Ligation for Incorporating EPR Spin Labels and Reporter Groups into RNA Katarzyna Wawrzyniak-Turek and Claudia Höbartner 5. A Flexible, Scalable Method for Preparation of Homogeneous Aminoacylated tRNAs Jinwei Zhang and Adrian R. Ferré-D'Amaré 6. Synthesis of A Biotinylated Photocleavable Nucleotide Monophosphate for the Preparation of Natively Folded RNAs. Yiling Luo, Herman O Sintim and T. Kwaku Dayie 7. Chemo-Enzymatic Synthesis of Selectively 13c/15n-Labeled Rna for Nmr Structural and Dynamics Studiess T. Kwaku Dayie, Luigi J. Alvarado, Andrew P. Longhini, Regan LeBlanc, Bin Chen, Cristoph Kreutz, Luigi J. Alvarado, Andrew P. Longhini, Regan LeBlanc, Bin Chen and Christoph Kreutz 8. RNA SHAPE Analysis of Small RNAs and Riboswitches Greggory M. Rice, Steven Busan, Fethullah Karabiber, Oleg V. Favorov , and Kevin M. Weeks. 9. Experimental Approaches for Measuring pKa's in RNA and DNA Pallavi Thaplyal and Philip C. Bevilacqua 10. Crystallographic Analysis of Tpp Riboswitch Binding by Small Molecule Ligands Discovered Through Fragment-Based Drug Discovery Approaches Katherine Deigan Warner and Adrian R. Ferré-D'Amaré 11. Methods for using New Conceptual Tools and Parameters to Assess RNA Structure by Small-Angle X-ray Scattering Francis E. Reyes, Camille R. Schwartz, John A. Tainer and Robert P. Rambo 12. Use of 19F NMR Methods to Probe Conformational Heterogeneity and Dynamics of Exchange in Functional RNA Molecules Caijie Zhao and Nancy L. Greenbaum 13. Site-Directed Spin-Labeling Strategies and Electron Paramagnetic Resonance Spectroscopy for Large Riboswitches Jackie M. Esquiaqui, Eileen M. Sherman, Jing-Dong Ye, and Gail E. Fanucci 14. Using sm-FRET and Denaturants to Reveal Folding Landscapes Euan Shaw, Patrick St-Pierre, Kaley McCluskey, Daniel A. Lafontaine and J. Carlos Penedo 15. Riboswitch Structure and Dynamics by smFRET Microscopy Krishna C. Suddala and Nils G. Walter 16. Ribosome Structure and Dynamics by smFRET Microscopy Bassem Shebl, Zenia Norman and Peter V. Cornish 17. Unraveling the Thermodynamics and Kinetics of RNA Assembly: Surface Plasmon Resonance, Isothermal Titration Calorimetry, and Circular Dichroism Charles G. Hoogstraten, Minako Sumita and Neil A. White 18. ITC Analysis of Ligand Binding to PreQ1 Riboswitches Joseph A. Liberman, Jarrod T. Bogue, Jermaine L. Jenkins, Mohammad Salim , and Joseph E. Wedekind. 19. Facile Characterization of Aptamer Kinetic and Equilibrium Binding Properties using Surface Plasmon Resonance Andrew L. Chang, Maureen McKeague and Christina D. Smolke 20. The AdoCbl-riboswitch Interaction Investigated by In-line Probing and Surface Plasmon Resonance (SPR) Spectroscopy Michelle F. Schaffer, Pallavi K. Choudhary and Roland K. O. Sigel 21. Assessing RNA Interactions with Proteins by DRaCALA Darshan K. Patel, Margo P. Gebbie and Vincent T. Lee
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