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

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’