Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part A

Edited By

  • Daniel Herschlag

This MIE volume provides laboratory techniques that aim to predict the structure of a protein which can have tremendous implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells.
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Researchers and students in cell, molecular and developmental biology


Book information

  • Published: November 2009
  • ISBN: 978-0-12-374399-2

Table of Contents

A. Chemical and Enzymatic Footprinting of RNA Structure
1. Equilibrium hydroxyl radical footprinting
2. Bench-top time-resolved hydroxyl radical footprinting
3. Analysis of hydroxyl radical footprinting gels ‘SAFA’
4. Kinetic modeling of reaction pathways from hydroxyl radical data
5. "BABE" mapping of protein/RNA position
6. Multiplexed….(MOHCA)
8. "In-line Probing"
10. Other NAIM
11. Purification of T7 RNA Polymerase
12. Purification of T4 RNA ligase
13. In vitro transcription of RNA
14. 32P-labeling of RNA
15. Fluorescent labeling of RNAs
16. Assembly of complex RNAs by ‘Moore-Sharp’ ligations
17. Assembly of complex RNAs by ‘Moore-Sharp’ ligations
18. General considerations for smFRET with RNA samples
19. Ion counting
21. NLPB
22. smNLPB
23. Gel mobility mapping of junction structure
24. Temperature gradient gels
25. Melting studies
26. Co-transcriptional folding studies
27. Activity assays to follow folding processes
28. 2AP fluorescence
29. EPR measurements of RNA dynamics
30. EPR measurements of RNA dynamics
31. FPA measurements of RNA dynamics
32. EPR methods to study specific metal ion binding sites in RNA
33. Thermodynamic study of site-specific metal ion binding sites in RNA
34. Oligonucleotide hybridization studies of RNA folding pathways
35. Native gel shifts
36. Tiling arrays to assess RNA structure
37. EPR distance measurements in RNA
38. RNA folding in vivo
39. Cleavage of RNAs with ‘restriction DNAzymes’