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Recommended Reading

• Peterman, E. J. G., Sosa, H. and Moerner, W. E. Single-molecule fluorescence spectroscopy and microscopy of biomolecular motors. Annual Review of Physical Chemistry 55: 79-96 (2004).
• Ha, T. Single-molecule fluorescence methods for the study of nucleic acids. Current Opinion in Structural Biology 11: 287-292 (2001).
• Haustein, E. and Schwille, P. Single-molecule spectroscopic methods. Current Opinion in Structural Biology 14: 531-540 (2004).
• Weiss, S. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nature Structural and Molecular Biology 7: 724-729 (2000).
• Ishijima, A. and Yanagida, T., Single molecule nanobioscience. Trends in Biochemical Sciences 26: 438-444 (2001).
• Roy, R., Hohng, S. and Ha, T. A practical guide to single-molecule FRET. Nature Methods 5: 507-516 (2008).
• Rhoades, E., Gussakovsky, E. and Haran, G. Watching proteins fold one molecule at a time. Proceedings of the National Academy of Sciences (USA) 100: 3197-3202 (2003).
• Moerner, W. E. and Fromm, D. P. Methods of single-molecule fluorescence spectroscopy and microscopy. Review of Scientific Instruments 74: 3597-3619 (2003).
• Weiss, S. Fluorescence spectroscopy of single biomolecules. Science 283: 1676-1683 (1999).
• Kural, C., Kim, H., Syed, S., Goshima, G., Gelfand, V. I. and Selvin, P. R. Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated movement? Science 308: 1469-1472 (2005).
• Lu, H. P., Xun, L. and Xie, X. S. Single-molecule enzymatic dynamics. Science 282: 1877-1882 (1998).
• Walter, N. G., Huang, C. Y., Manzo, A. J. and Sobhy, M. A. Do-it-yourself guide: how to use the modern single-molecule toolkit. Nature Methods 5: 475-489 (2008).
• Blum, C. and Subramaniam, V. Single-molecule spectroscopy of fluorescent proteins. Analytical and Bioanalytical Chemistry 393: 527-541 (2009).
• Churchman, L. S., Okten, Z., Rock, R. S., Dawson, J. F. and Spudich, J. A. Single molecule high resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proceedings of the National Academy of Sciences (USA) 102: 1419-1423 (2005).
• Garcia-Parajo, M. F., Veerman, J. A., Bouwhuis, R., Valleee, R. and Van Hulst, N. F. Optical probing of single fluorescent molecules and proteins. ChemPhysChem 2: 347-360 (2001).
• Gordon, M. P., Ha, T. and Selvin, P. R. Single-molecule high-resolution imaging with photobleaching. Proceedings of the National Academy of Sciences (USA) 101: 6462-6465 (2004).
• Ha, T. Single-molecule fluorescence resonance energy transfer. Methods 25: 78-86 (2001).

Additional Literature Sources

• Blum, C., Meixner, A. J. and Subramaniam, V. Spectral versatility of single reef coral fluorescent proteins detected by spectrally-resolved single molecule spectroscopy. ChemPhysChem 9: 310-315 (2008).
• Blum, C., Stracke, F., Becker, S., Millen, K. and Meixner, A. J. Discrimination and interpretation of spectral phenomena by room-temperature single-molecule spectroscopy. Journal of Physical Chemistry 105: 6983-6990 (2001).
• Bokinsky, G., Rueda, D., Misra, V. K., Rhodes, M. M., Gordus, A., Babcock, H. P., Walter, N. G. and Zhuang, X. Single-molecule transition-state analysis of RNA folding. Proceedings of the National Academy of Sciences (USA) 100: 9302-9307 (2003).
• Borisenko, V., Lougheed, T., Hesse, J., Fureder-Kitzumller, E., Fertig, N., Behrends, J. C., Woolley, G. A. and Schutz, G. J. Simultaneous optical and electrical recording of single gramicidin channels. Biophysical Journal 84: 612-622 (2003).
• Borsch, M., Diez, M., Zimmerman, B., Reuter, R. and Graber, P. Stepwise rotation of the y-subunit of EF0F1-ATP synthase observed by intramolecular single-molecule fluorescence resonance energy transfer. FEBS Letters 527: 147-152 (2002).
• Chirico, G., Cannone, F., Beretta, S., Diaspro, A., Campanini, B., Bettati, S., Ruotolo, R. and Mozzarelli, A. Dynamics of green fluorescent protein mutant2 in solution, on spin-coated glasses, and encapsulated in wet silica gels. Protein Science 11: 1152-1161 (2002).
• Cognet, L, Harms, G. S., Blab, G. A., Lommerse, P. H. M. and Schmidt, T. Simultaneous dual-color and dual-polarization imaging of single molecules. Applied Physics Letters 77: 4052-4054 (2000).
• Dahan, M., Levi, S., Luccardini, C., Rostaing, P., Riveau, B. and Triller, A. Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking. Science 302: 442-445 (2003).
• Deniz, A. A., Laurence, T. A., Beligere, G. S., Dahan, M., Martin, A. B., Chemla, D. S., Dawson, P. E., Schultz, P. G. and Weiss, S. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proceedings of the National Academy of Sciences (USA) 97: 5179-5184 (2000).
• Dickson, R. M., Norris, D. J., Tzeng, Y. L. and Moerner, W. E. Three-dimensional imaging of single molecules solvated in pores of poly(acrylamide) gels. Science 274: 966-969 (1996).
• Dittrich, P. S., Schafer, S. P. and Schwille, P. Characterization of the photoconversion on reaction of the fluorescent protein Kaede on the single-molecule level. Biophysical Journal 89: 3446-3455 (2005).
• Guignet, E. G., Segura, J. J., hovius, R. and Vogel, H. Repetitive reversible labeling of proteins at polyhistidine sequences for single-molecule imaging in live cells. ChemPhysChem 8: 1221-1227 (2007).
• Ha, T. Structural dynamics and processing of nucleic acids revealed by single-molecule spectroscopy. Biochemistry 43: 4055-4063 (2004).
• Ha, T., Laurence, T. A., Chemla, D. S. and Weiss, S. Polarization spectroscopy of single fluorescent molecules. Journal of Physical Chemistry B 103: 6839-6850 (1999).
• Ha, T., Rasnik, I., Cheng, W., Babcock, H. P., Gauss, G. H., Lohman, T. M. and Chu, S. Initiation and re-initiation of DNA unwinding by the Escherichia coli rep helicase. Nature 419: 638-641 (2002).
• Habuchi, S., Cotlet, M., Gronheid, R., Dirix, G., Michiels, J., Vanderleyden, J., De Schryver, F. C. and Hofkens, J. Single-molecule surface enhanced resonance Raman spectroscopy of the enhanced green fluorescent protein. Journal of the American Chemical Society 125: 8446-8447 (2003).
• Harms, G. S., Orr, G., Montal, M., Thrall, B. D., Colson, S. D. and Lu, H. P. Probing conformational changes of gramicidin ion channels by single-molecule patch-clamp fluorescence microscopy. Biophysical Journal 85: 1826-1838 (2003).
• Hintersteiner, M. and Auyer, M. Single-bead, single-molecule, single-cell fluorescence. Annals of the New York Academy of Sciences 1130: 1-11 (2008).
• Hohng, S. and Ha, T. Near-complete suppression of quantum dot blinking in ambient conditions. Journal of the American Chemical Society 126: 1324-1325 (2004).
• Hohng, S., Wilson, T. J., Tan, E., Clegg, R. M., Lilley, D. M. J. and Ha, T. Conformational flexibility of four-way junctions in RNA. Journal of Molecular Biology 336: 69-79 (2004).
• Ishijima, A., Kojima, H., Funatsu, T., Tokunaga, M., Higuchi, H., Tanaka, H. and Yanagida, T. Simultaneous observation of individual ATPase and mechanical events by a single myosin molecule during interaction with actin. Cell 92: 161-171 (1998).
• Jarvius, J., Melin, J., Goransson, J., Stenberg, J., Fredriksson, S., Gonzalez-Rey, C., Bertilsson, S. and Nilsson, M. Digital quantification using amplified single-molecule detection. Nature Methods 3: 725-727 (2006).
• Jung, C., Hellriegel, C., Michaelis, J. and Brauchle, C. Single-molecule traffic in mesoporous materials: translational, orientational, and spectral dynamics. Advanced Materials 19: 956-960 (2007).
• Jung, G., Wiehler, J., Gohde, W., Tittel, J., Basche, Th., Steipe, B. and Brauchle, C. Confocal microscopy of single molecules of the green fluorescent protein. Bioimaging 6: 54-61 (1998).
• Kapanidis, A. N. and Weiss, S. Fluorescent probes and bioconjugation chemistries for single molecule fluorescence analysis of biomolecules. Journal of Chemical Physics 117: 10953-10964 (2002).
• Kudryavtsev, V., Felekyan, S., Wozniak, A. K., Konig, M., Sandhagen, C., Kuhnemuth, R., Seidel, C. A. M. and Oesterhelt, F. Monitoring dynamic systems with multiparameter fluorescence imaging. Analytical and Bioanalytical Chemistry 387: 71-82 (2007).
• Lang, E., Baier, J. and Kohler, J. Epifluorescence, confocal and total internal reflection microscopy for single-molecule experiments: a quantitative comparison. Journal of Microscopy 222: 118-123 (2006).
• Lang, M. J., Fordyce, P. M. and Block, S. M. Combined optical trapping and single-molecule fluorescence. Journal of Biology 2: 6.1-6.4 (2003).
• Macklin, J. J., Trautman, J. K., Harris, T. D. and Brus, L. E. Imaging and time-resolved spectroscopy of single molecules at an interface. Science 272: 255-258 (1996).
• Margittai, M., Widengren, J., Shweinberger, E., Schroder, G. F., Felekyan, S., Haustein, E., Konig, M., Fasshauer, D., Grubmiller, H., Jahn, R. and Seidel, C. A. M. Single-molecule fluorescence resonance energy transfer reveals a dynamic equilibrium between closed and open conformations of syntaxin 1. Proceedings of the National Academy of Sciences (USA) 100: 15516-15521 (2003).
• Mashanov, G. I. and Molloy, J. E. Automatic detection of single fluorophores in live cells. Biophysical Journal 92: 2199-2211 (2007).
• Mashanov, G. I., Tacon, D., Knight, A. E., Peckham, M. and Molloy, J. E. Visualizing single molecules inside living cells using total internal reflection fluorescence microscopy. Methods 29: 142-152 (2003).
• McKinney, S. A., Declais, A. C., Lilley, D. M. J. and Ha, T. Structural dynamics of individual holliday junctions. Nature Structural and Molecular Biology 10: 93-97 (2003).
• Mutch, S. A., Fujimoto, B. S., Kuyper, C. L., Kuo, J. S., Bajialieh, S. M. and Chiu, D. T. Deconvolving single-molecule intensity distributions for quantitative microscopy measurements. Biophysical Journal 92: 2926-2943 (2007).
• Neuman, K. C. and Nagy, A. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nature Methods 5: 491-505 (2008).
• Nie, S., Chiu, D. T. and Zare, R. N. Probing Individual molecules with confocal fluorescence microscopy. Science 266: 1018-1021 (1994).
• Nie, S. and Zare, R. N. Optical detection of molecules. Annual Review of Biophysics and Biomolecular Structure 26: 567-596 (1997).
• Ober, R. J., Ram, S. and Ward, E.S. Localization accuracy in single-molecule microscopy. Biophysical Journal 86: 1185-1200 (2004).
• Rasnik, I., Myong, S., Cheng, W., Lohman, T. M. and Ha, T. DNA-binding orientation and domain conformation of the E. Coli rep helicase monomer bound to a partial duplex junction: single-molecule studies of fluorescently labeled enzymes. Journal of Molecular Biology 336: 395-408 (2004).
• Rothwell, P. J., Berger, S., Kensch, O., Felekyan, S., Antonik, M., Wohrl, B. M., Restle, T., Goody, R. S. and Seidel, C. A. M. Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes. Proceedings of the National Academy of Sciences (USA) 100: 1655-1660 (2003).
• Sako, Y. Imaging single molecules in living cells for systems biology. Molecular Systems Biology 2: 1-6 (2006).
• Sanchez-Mosteiro, G., Koopman, M., van Dijk, E. M. H. P., Hernando, J., van Hulst, N. F. and Garcia-Parajo, M.F. Photon antibunching proves emission from a single subunit in the autofluorescent protein DsRed. ChemPhyChem 5: 1782-1785 (2004).
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• Schuttrigkeit, T. A., Zachariae, U., von Feilitzsch, T., Wiehler, J., von Hummel, J., Steipe, B. and Michel-Beyerle, M. E. Picosecond time-resolved FRET in the fluorescent protein from Discosoma red (wt-DsRed). ChemPhysChem 2: 325-328 (2000).
• Schutz, G. J., Trabesinger, W. and Schmidt, T. Direct observation of ligand colocalization on individual receptor molecules. Biophysical Journal 74: 2223-2226 (1998).
• Shuler, B., Lipman, E. A. and Eaton, W. A. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature 419: 743-748 (2002).
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• Steinmeyer, R., Noskov. A., Krasel, C., Weber, I., Dees, C. and Harms, G. S. Improved fluorescent proteins for single-molecule research in molecular tracking and co-localization. Journal of Fluorescence 15: 707-721 (2005).
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• Tan, E., Wilson, T. J., Nahas, M. K., Clegg, R. M., Lilley, D. M. J. and Ha, T. A four-way junction accelerates hairpin riboyzme folding via a discrete intermediate. Proceedings of the National Academy of Sciences (USA) 100: 9308-9313 (2003).
• Tokunaga, M., Kitamura, K., Saito, K., Iwane, A. H. and Yanagida, T. Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy. Biochemical and Biophysical Research Communications 235: 47-53 (1997).
• Verbrugge, S., Kapitein, L. C. and Peterman, E. J. G. Kinesin moving through the spotlight: single-motor fluorescence microscopy with submillisecond time resolution. Biophysical Journal 92: 2536-2545 (2007).
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