Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B book cover

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

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.

Audience

Researchers and students in cell, molecular and developmental biology

Included in series
Methods in Enzymology

Hardbound, 502 Pages

Published: December 2009

Imprint: Academic Press

ISBN: 978-0-12-380922-3

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)
    7. SHAPE
    8. "In-line Probing"
    9. NAIM
    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
    B. BIOPHYSICAL TECHNIQUES
    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
    20. ASAXS
    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’

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