Riboswitch Discovery, Structure and Function: Volume 549

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.

Klappentext

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.

Inhalt

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