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

by Daniel Herschlag (Editor)

Overview

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. - Expert researchers introduce the most advanced technologies and techniques in protein structure and folding - Includes techniques on tiling assays

Product Details

ISBN-13:	9780123809230
Publisher:	Elsevier Science & Technology Books
Publication date:	11/16/2009
Series:	Methods in Enzymology , #469
Sold by:	Barnes & Noble
Format:	eBook
Pages:	502
File size:	7 MB

Table of Contents

A. Chemical and Enzymatic Footprinting of RNA Structure1. Equilibrium hydroxyl radical footprinting2. Bench-top time-resolved hydroxyl radical footprinting3. Analysis of hydroxyl radical footprinting gels 'SAFA'4. Kinetic modeling of reaction pathways from hydroxyl radical data5. "BABE" mapping of protein/RNA position6. Multiplexed….(MOHCA)7. SHAPE8. "In-line Probing" 9. NAIM10. Other NAIM11. Purification of T7 RNA Polymerase12. Purification of T4 RNA ligase13. In vitro transcription of RNA14. 32P-labeling of RNAB. BIOPHYSICAL TECHNIQUES15. Fluorescent labeling of RNAs16. Assembly of complex RNAs by 'Moore-Sharp' ligations17. Assembly of complex RNAs by 'Moore-Sharp' ligations 18. General considerations for smFRET with RNA samples19. Ion counting20. ASAXS 21. NLPB22. smNLPB23. Gel mobility mapping of junction structure24. Temperature gradient gels25. Melting studies26. Co-transcriptional folding studies27. Activity assays to follow folding processes28. 2AP fluorescence29. EPR measurements of RNA dynamics30. EPR measurements of RNA dynamics31. FPA measurements of RNA dynamics32. EPR methods to study specific metal ion binding sites in RNA33. Thermodynamic study of site-specific metal ion binding sites in RNA34. Oligonucleotide hybridization studies of RNA folding pathways35. Native gel shifts36. Tiling arrays to assess RNA structure37. EPR distance measurements in RNA38. RNA folding in vivo39. Cleavage of RNAs with 'restriction DNAzymes'

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From the Publisher

Time-tested and innovative methods aimed at helping researchers predict protein structure