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 fieldCovers research methods in biomineralization scienceContains 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 INDICE: 1. Using RNA-seq to identify cis- and trans-acting regulatory RNAs2. Riboswitch discovery by RNA-seq and differential 5'-end seq3. Discovering human adenosine-binding RNAs by structure-based bioinformatics and human genome-based in vitro selection.4. Exploiting the GlmS riboswitch for affinity purification of RNAs under non-denaturing conditions5. DNAzyme-mediated ligation for incorporating EPR spin-labels and reporter groups into RNA6. Synthesis of a biotinylated photocleavable nucleotide monophosphate for the preparation of natively folded RNAs7. Chemo-enzymatic synthesis of selectively 13C/15N-labeled RNA for NMR structural and dynamics studies8. Large-scale preparation of homogeneous aminoacylated tRNAs9. Structure and ligand interactions by crystallography, Small-angle X-ray scattering (SAXS) and isothermal titration calorimetry (ITC)10. Experimental Approaches for Measuring pKa's in RNA and DNA11. SHAPE analysis of small RNA12. Using smFRET and denaturants to reveal folding landscapes13. Using 19F methods to probe conformational heterogeneity and dynamics of exchange in model tetraloop systems and the human U2-U6 snRNA complex 14. Unraveling the thermodynamics and kinetics of RNA-RNA tertiary docking with surface plasmon resonance, isothermal titration calorimetry, and circular dichroism15. Structure by small-angle scattering (Nature paper introducing new conceptual tools and parameters)16. Riboswitch structure and dynamics by smFRET microscopy 17. RNA structure and dynamics by smFRET microscopy18. Studying Dynamics of Large Riboswitches using Site-Directed Spin Labeling and CW EPR19. Ligand interactions and thermodynamics by ITC20. RNA-Ligand interactions21. AdoCbl analog screen by in-line probing and surface plasmon resonance (SPR) spectroscopy22. Assessing RNA-ligand interactions by DRaCALA
- ISBN: 978-0-12-801122-5
- Editorial: Academic Press
- Encuadernacion: Cartoné
- Páginas: 514
- Fecha Publicación: 01/12/2014
- Nº Volúmenes: 1
- Idioma: Inglés