Riboswitch Discovery, Structure and Function

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.

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