RNA intramolecular dynamics by single-molecule FRET

Current Protocols in Nucleic Acid Chemistry

Volumn , Issue SUPPL. 34, 2008, Pages

  Hengesbach, Martin ^a   Kobitski, Andrei ^b   Voigts Hoffmann, Felix ^a   Frauer, Carina ^a   Nienhaus, G Ulrich ^b,c   Helm, Mark ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY OF ULM   (Germany)

^c University of Illinois at Urbana Champaign   (United States)

Author keywords

Dynamics; Fluorescence resonance energy transfer (FRET); Fluorescent dyes; Nucleotide modifications; RNA folding; Single molecule; Splint ligation

Indexed keywords

BIOTIN; CYANINE DYE 3; CYANINE DYE 5; DEOXYRIBONUCLEOTIDE; FLUORESCEIN; FLUORESCENT DYE; OLIGORIBONUCLEOTIDE; PHOSPHORAMIDOUS ACID DERIVATIVE; TETRAMETHYLRHODAMINE;

BIOTINYLATION; BLEACHING; CONFOCAL LASER MICROSCOPY; DNA MODIFICATION; DNA RNA HYBRIDIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENCE SPECTROSCOPY; INTERMETHOD COMPARISON; LASER; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NUCLEIC ACID ANALYSIS; PHOSPHORYLATION; PHOTON; PRIORITY JOURNAL; QUANTUM YIELD; REVIEW; RNA BINDING; RNA CONFORMATION; RNA STABILITY; RNA STRUCTURE; RNA SYNTHESIS; SOLID PHASE SYNTHESIS; SOLVENT EFFECT; SPECTROSCOPY; STOICHIOMETRY; THERMODYNAMICS;

EID: 58849135321     PISSN: 19349270     EISSN: 19349289     Source Type: Journal    
DOI: 10.1002/0471142700.nc1112s34     Document Type: Review

References (51)

1. Aitken, C.E., Marshall, R.A., and Puglisi, J.D. 2007. An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys. J. 94:1826-1835.
2. Amirgoulova, E.V., Groll, J., Heyes, C.D., Ameringer, T., Röcker, C., Möller, M., and Nienhaus, G.U. 2004. Biofunctionalized polymer surfaces exhibiting minimal interaction towards immobilized proteins. Chemphyschem 5:552-555.
3. Bassi, G.S., Murchie, A.I., Walter, F., Clegg, R.M., and Lilley, D.M. 1997. Ion-induced folding of the hammerhead ribozyme: A fluorescence resonance energy transfer study. EMBO J. 16:7481-7489.
4. Chan, B.,Weidemaier, K., Yip, W.T., Barbara, P.F., and Musier-Forsyth, K. 1999. Intra-tRNA distance measurements for nucleocapsid proteindependent tRNA unwinding during priming of HIV reverse transcription. Proc. Natl. Acad. Sci. U.S.A. 96:459-464.
5. Clegg, R.M. 1992. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211:353-388.
6. Coban, O., Lamb, D.C., Zaychikov, E., Heumann, H., and Nienhaus, G.U. 2006. Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy. Biophys. J. 90:4605-4617.
7. Deniz, A.A., Dahan, M., Grunwell, J.R., Ha, T., Faulhaber, A.E., Chemla, D.S., Weiss, S., and Schultz, P.G. 1999. Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Forster distance dependence and subpopulations. Proc. Natl. Acad. Sci. U.S.A. 96:3670-3675.
8. Dietrich, A., Buschmann, V., Müller, C., and Sauer, M. 2002. Fluorescence resonance energy transfer (FRET) and competing processes in donoracceptor substituted DNA strands: A comparative study of ensemble and single-molecule data. J. Biotechnol. 82:211-231.
9. Groll, J., Amirgoulova, E.V., Ameringer, T., Heyes, C.D., Röcker, C., Nienhaus, G.U., and Möller, M. 2004. Biofunctionalized, ultrathin coatings of cross-linked star-shaped poly(ethylene oxide) allowreversible folding of immobilized proteins. J. Am. Chem. Soc. 126:4234-4239.
10. Ha, T., Enderle, T., Ogletree, D.F., Chemla, D.S., Selvin, P.R., and Weiss, S. 1996. Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl. Acad. Sci. U.S.A. 93:6264-6268.
11. Ha, T., Zhuang, X., Kim, H.D., Orr, J.W., Williamson, J.R., and Chu, S. 1999. Ligandinduced conformational changes observed in single RNA molecules. Proc. Natl. Acad. Sci. U.S.A. 96:9077-9082.
12. Heyes, C.D., Kobitski, A.Y., and Nienhaus, G.U. 2004. Biocompatible surfaces for specific tethering of individual protein molecules. J. Phys. Chem. B 108:13387-13394.
13. Heyes, C.D., Groll, J., Möller, M., and Nienhaus, G.U. 2007. Synthesis, patterning and applications of star-shaped poly(ethylene glycol) biofunctionalized surfaces. Mol. Biosyst. 3:419-430.
14. Huang, Z., Ji, D., Xia, A.D., Koberling, F., Patting, M., and Erdmann, R. 2005. Direct observation of delayed fluorescence from a remarkable back-isomerization in Cy5. J. Am. Chem. Soc. 127:8064-8066.
15. Ishii, Y., Yoshida, T., Funatsu, T., Wazawa, T., and Yanagida, T. 1999. Fluorescence resonance energy transfer between single fluorophores attached to a coiled-coil protein in aqueous solution. Chem. Phys. 247:163-173.
16. Jares-Erijman, E.A. and Jovin, T.M. 2003. FRET imaging. Nat. Biotechnol. 21:1387-1395.
17. Kapanidis, A.N., Lee, N.K., Laurence, T.A., Doose, S., Margeat, E., and Weiss, S. 2004. Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules. Proc. Natl. Acad. Sci. U.S.A. 101:8936-8941.
18. Kim, H.D., Nienhaus, G.U., Ha, T., Orr, J.W., Williamson, J.R., and Chu, S. 2002. Mg2+- dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc.Natl. Acad. Sci. U.S.A. 99:4284-4289.
19. Klostermeier, D. and Millar, D.P. 2001. Tertiary structure stability of the hairpin ribozyme in its natural and minimal forms: Different energetic contributions from a ribose zipper motif. Biochemistry 40:11211-11218.
20. Kobitski, A.Y., Nierth, A., Helm, M., Jäschke, A., and Nienhaus, G.U. 2007. Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis. Nucleic Acids Res. 35:2047-2059.
21. Kurschat, W.C., Muller, J., Wombacher, R., and Helm, M. 2005. Optimizing splinted ligation of highly structured small RNAs. RNA 11:1909-1914.
22. Kuzmenkina, E.V., Heyes, C.D., and Nienhaus, G.U. 2005. Single-molecule Forster resonance energy transfer study of protein dynamics under denaturing conditions. Proc. Natl. Acad. Sci. U.S.A. 102:15471-15476.
23. Lakowicz, J.R. 2006. Principles of Fluorescence Spectroscopy. Springer, New York.
24. Lee, N.K., Koh, H.R., Han, K.Y., and Kim, S.K. 2007. Folding of 8-17 deoxyribozyme studied by three-color alternating-laser excitation of single molecules. J. Am. Chem. Soc. 129:15526-15534.
25. McKinney, S.A., Declais, A.C., Lilley, D.M., and Ha, T. 2003. Structural dynamics of individual Holliday junctions. Nat. Struct. Biol. 10:93-97.
26. Mujumdar, R.B., Ernst, L.A., Mujumdar, S.R., Lewis, C.J., and Waggoner, A.S. 1993. Cyanine dye labeling reagents: Sulfoindocyanine succinimidyl esters. Bioconjug. Chem. 4:105-111.
27. Murchie, A.I., Thomson, J.B.,Walter, F., and Lilley, D.M. 1998. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell 1:873-881.
28. Nienhaus, G.U. 2006. Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis. Macromol. Biosci. 6:907-922.
29. Panchuk-Voloshina, N., Haugland, R.P., Bishop-Stewart, J., Bhalgat, M.K., Millard, P.J., Mao, F., Leung,W.Y., and Haugland, R.P. 1999. Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates. J. Histochem. Cytochem. 47:1179-1188.
30. Pinard, R., Hampel, K.J., Heckman, J.E., Lambert, D., Chan, P.A., Major, F., and Burke, J.M. 2001. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J. 20:6434-6442.
31. Qin, P.Z. and Pyle, A.M. 1999. Site-specific labeling of RNA with fluorophores and other structural probes. Methods 18:60-70.
32. Rasnik, I., McKinney, S.A., and Ha. T. 2005. Surfaces and orientations: Much to FRET about? Acc. Chem. Res. 38:542-548.
33. Rasnik, I., McKinney, S.A., and Ha, T. 2006. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat. Methods 3:891-893.
34. Rothwell, P.J., Berger, S., Kensch, O., Felekyan, S., Antonik, M., Wöhrl, B.M., Restle, T., Goody, R.S., and Seidel, C.A. 2003. Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:pRimer/template complexes. Proc. Natl. Acad. Sci. U.S.A. 100:1655-1660.
35. Sabanayagam, C.R., Eid, J.S., and Meller, A. 2005. Using fluorescence resonance energy transfer to measure distances along individual DNA molecules: Corrections due to nonideal transfer. J. Chem. Phys. 122:061103.
36. Scaringe, S.A., Wincott, F.E., and Caruthers, M.H. 1998. Novel RNA synthesis method using 5′-Silyl-2′-Orthoester protecting groups. J. Am. Chem. Soc. 120:11820-11821.
37. Selvin, P.R. 2000. The renaissance of fluorescence resonance energy transfer. Nat. Struct. Biol. 7:730-734.
38. Singh, K.K., Parwaresch, R., and Krupp, G. 1999. Rapid kinetic characterization of hammerhead ribozymes by real-time monitoring of fluorescence resonance energy transfer (FRET). RNA 5:1348-1356.
39. Slatko, B.E. and Albright, L.M. 2001. Denaturing gel electrophoresis for sequencing. Curr. Protoc. Mol. Biol. 16:7.6.1-7.6.13.
40. Tan, E., Wilson, T.J., Nahas, M.K., Clegg, R.M., Lilley, D.M.J, and Ha, T. 2003. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl. Acad. Sci. U.S.A. 100:9308-9313.
41. Telser, J., Cruickshank, K.A., Morrison, L.E., and Netzel, T.L. 1989. Synthesis and characterization of DNA oligomers and duplexes containing covalently attached molecular labels: Comparison of biotin, fluorescein, and pyrene labels by thermodynamic and optical spectroscopic measurements. J. Am. Chem. Soc. 111:6966.
42. Tuschl, T., Gohlke, C., Jovin, T.M.,Westhof, E., and Eckstein, F. 1994. A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements. Science 266:785-789.
43. Voigts-Hoffmann, F., Hengesbach, M., Kobitski, A.Y., van Aerschot, A., Herdewijn, P., Nienhaus, G.U., and Helm, M. 2007. A methyl group controls conformational equilibrium in human mitochondrial tRNA(Lys). J. Am. Chem. Soc. 129:13382-13383.
44. von Ahsen, U. and Noller, H.F. 1995. Identification of bases in 16S rRNAessential for tRNAbinding at the 30S ribosomal P site. Science 267:234-237.
45. Walter, N.G., Hampel, K.J., Brown, K.M., and Burke, J.M. 1998. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J. 17:2378-2391.
46. Walter, N.G., Burke, J.M., and Millar, D.P. 1999. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nat. Struct. Biol. 6:544-549.
47. Walter, N.G., Yang, N., and Burke, J.M. 2000. Probing non-selective cation binding in the hairpin ribozyme with Tb(III). J. Mol. Biol. 298:539-555.
48. Walter, N.G., Chan, P.A., Hampel, K.J., Millar, D.P., and Burke, J.M. 2001. A base change in the catalytic core of the hairpin ribozyme perturbs function but not domain docking. Biochemistry 40:2580-2587.
49. Widengren, J. and Schwille, P. 2000. Characterization of photo-induced isomerization and backisomerization of the cyanine dye Cy5 by fluorescence correlation spectroscopy. J. Phys. Chem. 104:6416-6428.
50. Zhuang, X., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T., Herschlag, D., and Chu S. 2000. A single-molecule study of RNA catalysis and folding. Science 288:2048-2051.
51. Zhuang, X., Kim, H., Pereira, M.J., Babcock, H.P., Walter, N.G., and Chu, S. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science 296:1473-1476.