Measuring the Energetic Coupling of Tertiary Contacts in RNA Folding using Single Molecule Fluorescence Resonance Energy Transfer

Methods in Enzymology

Volumn 472, Issue , 2010, Pages 205-220

  Greenfeld, Max ^a,b   Herschlag, Daniel ^a,b  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXPERIMENTAL DESIGN; FLUORESCENCE RESONANCE ENERGY TRANSFER; PROTEIN CONFORMATION; RNA FOLDING; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METHODOLOGY; THERMODYNAMICS;

RNA;

FLUORESCENCE RESONANCE ENERGY TRANSFER; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS;

MLCS; MLOWN;

EID: 77957066586     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)72009-7     Document Type: Chapter

References (38)

1. Akiyama, B.M., Stone, M.D., Assembly of complex RNAs by splinted ligation. Methods Enzymol. 469 (2009), 27–46.
2. Bai, Y., Das, R., Millett, I., Herschlag, D., Doniach, S., Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc. Natl. Acad. Sci. USA 102 (2005), 1035–1040.
3. Bai, Y., Greenfeld, M., Travers, K.J., Chu, V.B., Lipfert, J., Doniach, S., Herschlag, D., Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J. Am. Chem. Soc. 129 (2007), 14981–14988.
4. Bartley, L.E., Zhuang, X.W., Das, R., Chu, S., Herschlag, D., Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. J. Mol. Biol. 328 (2003), 1011–1026.
5. Baum, D.A., Silverman, S.K., Deoxyribozyme-catalyzed labeling of RNA. Angew. Chem. Int. Ed. 46 (2007), 3502–3504.
6. Boukobza, E., Sonnenfeld, A., Haran, G., Immobilization in surface-tethered lipid vesicles as a new tool for single biomolecule spectroscopy. J. Phys. Chem. B 105 (2001), 12165–12170.
7. Cruz, J.A., Westhof, E., The dynamic landscapes of RNA architecture. Cell 136 (2009), 604–609.
8. 2+ stoichiometry for folding an RNA metal ion core. J. Am. Chem. Soc. 127 (2005), 8272–8273.
9. Ditzler, M.A., Rueda, D., Mo, J.J., Hakansson, K., Walter, N.G., A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res. 36 (2008), 7088–7099.
10. Dorywalska, M., Blanchard, S.C., Gonzalez, R.L., Kim, H.D., Chu, S., Puglisi, J.D., Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res. 33 (2005), 182–189.
11. Draper, D.E., A guide to ions and RNA structure. RNA 10 (2004), 335–343.
12. Elenko, M.P., Szostak, J.W., van Oijen, A.M., Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics. J. Am. Chem. Soc. 131 (2009), 9866–9867.
13. 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc. Natl. Acad. Sci. USA 103 (2006), 14003–14008.
14. Ha, T., Zhuang, X.W., Kim, H.D., Orr, J.W., Williamson, J.R., Chu, S., Ligand-induced conformational changes observed in single RNA molecules. Proc. Natl. Acad. Sci. USA 96 (1999), 9077–9082.
15. Hodak, J.H., Fiore, J.L., Nesbitt, D.J., Downey, C.D., Pardi, A., Docking kinetics and equilibrium of a GAAA tetra loop-receptor motif probed by single-molecule FRET. Proc. Natl. Acad. Sci. USA 102 (2005), 10505–10510.
16. Huang, Z., Pei, W.M., Han, Y., Jayaseelan, S., Shekhtman, A., Shi, H., Niu, L., One RNA aptamer sequence, two structures: A collaborating pair that inhibits ampa receptors. Nucleic Acids Res. 37 (2009), 4022–4032.
17. Jencks, W.P., On the attribution and additivity of binding-energies. Proc. Natl. Acad. Sci. USA 78 (1981), 4046–4050.
18. Joo, C., Ha, T., Single-molecule FRET with total internal reflection microscopy. Single Molecule Techniques: A Laboratory Manual, 2008 pp. 3–36.
19. Joo, C., Balci, H., Ishitsuka, Y., Buranachai, C., Ha, T., Advances in single-molecule fluorescence methods for molecular biology. Annu. Rev. Biochem. 77 (2008), 51–76.
20. Korennykh, A.V., Plantinga, M.J., Correll, C.C., Piccirilli, J.A., Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin. Biochemistry 46 (2007), 12744–12756.
21. Li, P.T.X., Vieregg, J., Tinoco, I., How RNA unfolds and refolds. Annu. Rev. Biochem. 77 (2008), 77–100.
22. Mammen, M., Choi, S.K., Whitesides, G.M., Polyvalent interactions in biological systems: Implications for design and use of multivalent ligands and inhibitors. Angew. Chem. Int. Ed. 37 (1998), 2755–2794.
23. McKinney, S.A., Joo, C., Ha, T., Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J. 91 (2006), 1941–1951.
24. Noller, H.F., RNA structure: Reading the ribosome. Science 309 (2005), 1508–1514.
25. Okumus, B., Wilson, T.J., Lilley, D.M.J., Ha, T., Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. J. Phys. Chem. B 87 (2004), 2798–2806.
26. Pereira, M.J.B., Nikolova, E.N., Hiley, S.L., Jaikaran, D., Collins, R.A., Walter, N.G., Single vs ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J. Mol. Biol. 382 (2008), 496–509.
27. Roy, R., Hohng, S., Ha, T., A practical guide to single-molecule FRET. Nat. Methods 5 (2008), 507–516.
28. Sattin, B., Zhao, W., Travers, K., Chut, S., Herschlag, D., Direct measurement of tertiary contact cooperativity in RNA folding. J. Am. Chem. Soc. 130 (2008), 6085–6087.
29. Smith, G.J., Sosnick, T.R., Scherer, N.F., Pan, T., Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA 11 (2005), 234–239.
30. Smith, G.J., Lee, K.T., Qu, X.H., Xie, Z., Pesic, J., Sosnick, T.R., Pan, T., Scherer, N.F., A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics. J. Mol. Biol. 378 (2008), 943–953.
31. Solomatin, S., Herschlag, D., Methods of site-specific labeling of RNA with fluorescent dyes. Methods Enzymol. 469 (2009), 47–68.
32. Solomatin, S.V., Greenfeld, M., Chu, S., Herschlag, D., Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature 463 (2010), 681–684.
33. Stone, M.D., Mihalusova, M., O'Connor, C.M., Prathapam, R., Collins, K., Zhuang, X.W., Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein. Nature 446 (2007), 458–461.
34. Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., Chance, M.R., Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J. Mol. Biol. 343 (2004), 1195–1206.
35. Tan, E., Wilson, T.J., Nahas, M.K., Clegg, R.M., Lilley, D.M.J., Ha, T., A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl. Acad. Sci. USA 100 (2003), 9308–9313.
36. Williamson, J.R., Cooperativity in macromolecular assembly. Nat. Chem. Biol. 4 (2008), 458–465.
37. Zhuang, X.W., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T.J., Herschlag, D., Chu, S., A single-molecule study of RNA catalysis and folding. Science 288 (2000), 2048–2051.
38. Zhuang, X.W., Kim, H., Pereira, M.J.B., Babcock, H.P., Walter, N.G., Chu, S., Correlating structural dynamics and function in single ribozyme molecules. Science 296 (2002), 1473–1476.