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

<p>A. Chemical and Enzymatic Footprinting of RNA Structure<br>1. Equilibrium hydroxyl radical footprinting<br>2. Bench-top time-resolved hydroxyl radical footprinting<br>3. Analysis of hydroxyl radical footprinting gels ‘SAFA’<br>4. Kinetic modeling of reaction pathways from hydroxyl radical data<br>5. "BABE" mapping of protein/RNA position<br>6. Multiplexed….(MOHCA)<br>7. SHAPE<br>8. "In-line Probing" <br>9. NAIM<br>10. Other NAIM<br>11. Purification of T7 RNA Polymerase<br>12. Purification of T4 RNA ligase<br>13. In vitro transcription of RNA<br>14. 32P-labeling of RNA<br>B. BIOPHYSICAL TECHNIQUES<br>15. Fluorescent labeling of RNAs<br>16. Assembly of complex RNAs by ‘Moore-Sharp’ ligations<br>17. Assembly of complex RNAs by ‘Moore-Sharp’ ligations <br>18. General considerations for smFRET with RNA samples<br>19. Ion counting<br>20. ASAXS <br>21. NLPB<br>22. smNLPB<br>23. Gel mobility mapping of junction structure<br>24. Temperature gradient gels<br>25. Melting studies<br>26. Co-transcriptional folding studies<br>27. Activity assays to follow folding processes<br>28. 2AP fluorescence<br>29. EPR measurements of RNA dynamics<br>30. EPR measurements of RNA dynamics<br>31. FPA measurements of RNA dynamics<br>32. EPR methods to study specific metal ion binding sites in RNA<br>33. Thermodynamic study of site-specific metal ion binding sites in RNA<br>34. Oligonucleotide hybridization studies of RNA folding pathways<br>35. Native gel shifts<br>36. Tiling arrays to assess RNA structure<br>37. EPR distance measurements in RNA<br>38. RNA folding in vivo<br>39. Cleavage of RNAs with ‘restriction DNAzymes’ </p>