Abstract
Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy.
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References
Abelson J et al (2010) Conformation dynamics of single pre-mRNA molecules in spliceosome assembly. Nat Struct Mol Biol 17:504–512
Aitken CE, Petrov A, Puglisi JD (2010) Single ribosome dynamics and the mechanism of translation. Annu Rev Biophys 39:491–513
Alemán EA, Silva Cd, Patrich EM, Musier-Forsyth K, Rueda D (2014) Single-molecule fluorescence using nucleotide analogues: a proof-of-principle. J Phys Chem Lett 5:777–781
Alvarez-Dominguez JR et al (2014) Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood 123:570–581
Axelrod D, Burghardt TP, Thompson NL (1984) Total internal reflection fluorescence. Annu Rev Biophys Bioeng 13:247–268
Banerjee PR, Deniz AA (2014) Shedding light on protein folding landscapes by single molecule fluorescence. Chem Soc Rev 43:1172–1188
Bath J, Turberfield AJ (2007) DNA nanomachines. Nat Nanotechnol 2:275–284
Batista PJ, Chang HY (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell 152:1298–1307
Bokinsky G et al (2003) Single-molecule transition-state analysis of RNA folding. Proc Natl Acad Sci USA 100:9302–9307
Breaker RR (2011) Prospects for riboswitch discovery and analysis. Mol Cell 43:867–879
Cha T-G, Pan J, Chen H, Salgado J, Li X, Mao C, Choi JH (2014) A synthetic DNA motor that transports nanoparticles along carbon nanotubes. Nat Nanotechnol 9:39–43
Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A (2011) Femtosecond X-ray protein nanocrystallography. Nature 470:73–77
Chen C et al (2011) Single-molecule fluorescence measurements of ribosomal translocation dynamics. Mol Cell 42:367–377
Chen J, Tsai A, O’Leary SE, Petrov A, Puglisi JD (2012) Unraveling the dynamics of ribosome translocation. Curr Opin Struc Biol 22:804–814
Chong S, Min W, Xie XS (2010) Ground-state depletion microscopy: detection sensitivity of single-molecule optical absorption at room temperature. J Phys Chem Lett 1:3316–3322
Churchman LS, Ökten Z, Rock RS, Dawson JF, Spudich JA (2005) Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proc Natl Acad Sci USA 102:1419–1423
Crawford R, Torella JP, Aigrain L, Plochowietz A, Gryte K, Uphoff S, Kapanidis AN (2013) Long-lived intracellular single-molecule fluorescence using electroporated molecules. Biophys J 105:2439–2450
Darzacq X, Shav-Tal Y, de Turris V, Brody Y, Shenoy SM, Phair RD, Singer RH (2007) In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 14:796–806
Ditzler MA, Rueda D, Mo J, Hakansson K, Walter NG (2008) A rugged free energy landscap separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res 36:7088–7099
Djebali S et al (2012) Landscape of transcription in human cells. Nature 489:101–108
Dupuis NF, Holmstrom ED, Nesbitt DJ (2014) Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics. Proc Natl Acad Sci USA 111:8464–8469
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138
Elting MW et al (2013) Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC). Opt Express 21:1189–1202
English BP et al (2006) Ever-fluctuating single enzyme molecules: Michaelis–Menten equation revisited. Nat Chem Biol 2:87–94
Ferreon ACM, Moran CR, Ferreon JC, Deniz AA (2010) Alteration of the α-synuclein folding landscape by a mutation related to Parkinson’s disease. Angew Chem Int Ed 49:3469–3472
Ferreon ACM, Ferreon JC, Wright PE, Deniz AA (2013) Modulation of allostery by protein intrinsic disorder. Nature 498:390–394
Feynman RP (1963) Rachet and pawl. The Feynman lectures on physics, vol 1. Addison-Wesley, Massachusetts, pp 1–7
Feynmann RP (1961) Miniaturization. Reinhold Publishing Corporation, New York
Fu J et al (2014) Multi-enzyme complexes on DNA scaffolds capable of substrate channeling with an artificial swinging arm. Nat Nanotechnol 9:531–536
Gahlmann A, Moerner WE (2014) Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging. Nat Rev Microbiol 12:9–22
Gaiduk A, Yorulmaz M, Ruijgrok PV, Orrit M (2010) Room-temperature detection of a single molecule’s absorption by photothermal contrast. Science 330:353–356
Gorris HH, Rissin DM, Walt DR (2007) Stochastic inhibitor release and binding from single-enzyme molecules. Proc Natl Acad Sci USA 104:17680–17685
Grunwald D, Singer RH (2010) In vivo imaging of labelled endogenous beta-actin mRNA during nucleocytoplasmic transport. Nature 467:604–607
Grunwald D, Singer RH, Rout M (2011) Nuclear export dynamics of RNA-protein complexes. Nature 475:333–341
Ha T, Tinnefeld P (2012) Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annu Rev Phys Chem 63:595–617
Harada T et al (2014) Activatable organic near-infrared fluorescent probes based on a bacteriochlorin platform: synthesis and multicolor in vivo imaging with a single excitation. Bioconjug Chem 25:362–369
He Y, Liu DR (2010) Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nat Nanotechnol 5:778–782
Hoskins AA et al (2011) Ordered and dynamic assembly of single spliceosomes. Science 331:1289–1295
Huang B, Wang W, Bates M, Zhuang X (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810–813
Hyeon C, Lee J, Yoon J, Hohng S, Thirumalai D (2012) Hidden complexity in the isomerization dynamics of Holliday junctions. Nat Chem 4:907–914
Ito Y, Fukusaki E (2004) DNA as a ‘Nanomaterial’. J Mol Catal B-Enzym 28:155–166
Johnson-Buck A, Walter NG (2014) Discovering anomalous hybridization kinetics on DNA nanostructures using single-molecule fluorescence microscopy. Methods 67:177–184
Johnson-Buck A, Nangreave J, Kim D, Bather M, Yan H, Walter NG (2013) Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Lett 13:728–733
Joo C, Balci H, Ishitsuka Y, Buranachai C, Ha T (2008) Advances in single-molecule fluorescence methods for molecular biology. Annu Rev Biochem 77:51–76
Juette MF, Terry DS, Wasserman MR, Zhou Z, Altman RB, Zheng Q, Blanchard SC (2014) The bright future of single-molecule fluorescence imaging. Curr Opin Chem Biol 20C:103–111
Jungmann R, Scheible M, Simmel FC (2012) Nanoscale imaging in DNA nanotechnology. WIREs Nanomed Nanobiotechnol 4:66–81
Jungmann R, Avendano MS, Woehrstein JB, Dai M, Shih WM, Yin P (2014) Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat Methods 11:313–318
Kalo A, Kafri P, Shav-Tal Y (2013) Single mRNP tracking in living mammalian cells. Methods Mol Biol 1042:87–99
Kellenberger CA, Wilson SC, Sales-Lee J, Hammond MC (2013) RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP–GMP. J Am Chem Soc 135:4906–4909
Keryer-Bibens C, Barreau C, Osborne HB (2008) Tethering of proteins to RNAs by bacteriophage proteins. Biol Cell 100:125–138
König SLB, Liyanage PS, Sigel RKO, Rueda D (2013) Helicase-mediated changes in RNA structure at the single-molecule level. RNA Biol 10:133–148
Kretz M et al (2013) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493:231–235
Krishnan R, Blanco MR, Kahlscheuer ML, Abelson J, Guthrie C, Walter NG (2013) Biased Brownian racheting leads to pre-mRNA remodeling and capture prior to first-step splicing. Nat Struct Mol Biol 20:1450–1457
Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11:597–610
Kukura P, Celebrano M, Renn A, Sandoghdar V (2010) Single-molecule sensitivity in optical absorption at room temperature. J Phys Chem Lett 1:3323–3327
Küpper J, Stern S, Holmegaard L, Filsinger F, Rouzée A, Rudenko A (2014) X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser. Phys Rev Lett 112:083002
Lackowickz JR (2007) Principles of fluorescence spectroscopy, 3rd edn. Springer, New York City
Lee JT, Bartolomei MS (2013) X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 152:1308–1323
Lee W, Jose D, Phelps C, Marcus AH, Hippel PHv (2013) A single-molecule view of the assembly pathway, subunit stoichiometry, and unwinding activity of the bacteriophage T4 primosome (helicase-primase) complex. Biochemistry-US 52:3157–3170
Li GW, Xie XS (2011) Central dogma at the single-molecule level in living cells. Nature 475:308–315
Lin C et al (2012) Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat Chem 4:832–839
Liu S, Bokinsky G, Walter NG, Zhuang X (2007) Dissecting the multi-step reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting”. Proc Natl Acad Sci USA 104:12634–12639
Liu B, Baskin RJ, Kowalczykowski SC (2013) DNA unwinding heterogeneity by RecBCD results from static molecules unable to equilibrate. Nature 500:482–485
Lu Y, Liu J (2006) Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr Opin Biotech 17:580–588
Lu HP, Xun L, Xie XS (1998) Single-molecule enzyme dynamics. Science 282:1877–1882
Lund K et al (2010) Molecular robots guided by prescriptive landscapes. Nature 465:206–210
Ma J, Yang W (2010) Three-dimensional distribution of transient interactions in the nuclear pore complex obtained from single-molecule snapshots. Proc Natl Acad Sci USA 107:7305–7310
Ma J et al (2013) High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat Commun 4:2414
Marek MS, Johnson-Buck A, Walter NG (2011) The shape-shifting quasispecies of RNA: one sequence, many functional folds. Phys Chem Chem Phys 13:11524–11537
Martin RM, Rino J, Carvalho C, Kirchhausen T, Carmo-Fonseca M (2013) Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep 4:1144–1155
McDowell SE, Jun JM, Walter NG (2010) Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations. RNA 16:2414–2426
Michelotti N, de Silva C, Johnson-Buck AE, Manzo AJ, Walter NG (2010) Chapter six—A bird’s eye view: tracking slow nanometer-scale movements of single molecular nano-assemblies. In: Walter NG (ed) Methods in enzymology, vol 475. Academic Press, London, pp 121–148
Michelotti N, Johnson-Buck A, Manzo AJ, Walter NG (2012) Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology. WIREs Nanomed Nanobiotechnol 4:139–152
Mor A, Ben-Yishay R, Shav-Tal Y (2010) On the right track: following the nucleo-cytoplasmic path of an mRNA. Nucleus 1:492–498
Nienhaus K, Nienhaus GU (2014) Fluorescent proteins for live-cell imaging with super-resolution. Chem Soc Rev 43:1088–1106
Omabegho T, Sha R, Seeman NC (2009) A bipedal DNA Brownian motor with coordinated legs. Science 324:67–71
Paige JS, Nguyen-Duc T, Song W, Jaffrey SR (2012) Fluorescence imaging of cellular metabolites with RNA. Science 335:1194
Park HY et al (2014) Visualization of dynamics of single endogenous mRNA labeled in live mouse. Science 343:422–424
Patterson G, Davidson M, Manley S, Lippincott-Schwartz J (2010) Superresolution imaging using single-molecule localization. Annu Rev Phys Chem 61:345–367
Pereira MJB, Nikolova EN, Hiley SL, Jaikaran D, Collins RA, Walter NG (2008) Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J Mol Biol 382:496–509
Perez-Jimenez R et al (2011) Single-molecule paleoenzymology probes the chemistry of resurrected enzymes. Nat Struct Mol Biol 18:592–596
Phelps C, Lee W, Jose D, Hippel PHv, Marcus AH (2013) Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions. Proc Natl Acad Sci USA 110:17320–17325
Pitchiaya S, Androsavich JR, Walter NG (2012) Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly. EMBO Rep 13:709–715
Pitchiaya S, Krishnan V, Custer TC, Walter NG (2013) Dissecting non-coding RNA mechanisms in cellulo by single-molecule high-resolution localization and counting. Methods 63:188–199
Pitchiaya S, Heinicke LA, Custer TC, Walter NG (2014) Single-molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 114:3224
Prasher DC, Eckenrode VK, Ward WW, Prendergast FG, Cormier MJ (1992) Primary structure of the Aequorea victoria green-fluorescent protein. Gene 111:229–233
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S (2006) Stochastic mRNA synthesis in mammalian cells. PLoS Biol 4:e309
Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166
Robinson A, van Oijen AM (2013) Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies. Nat Rev Microbiol 11:303–315
Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302
Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5:507–516
Rueda D, Walter NG (2005) Single molecule fluorescence control for nanotechnology. J Nanosci Nanotechnol 5:1–11
Rueda D, Bokinsky G, Rhodes MM, Rust MJ, Zhuang X, Walter NG (2004) Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proc Natl Acad Sci USA 101:10066
Seeman NC (2003) DNA in a material world. Nature 421:427–431
Sengupta P, Van Engelenburg S, Lippincott-Schwartz J (2012) Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 23:1092–1102
Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL, Singer RH (2004) Dynamics of single mRNPs in nuclei of living cells. Science 304:1797–1800
Shimomura O, Johnson FH, Saiga Y (1962) Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea. J Cell Comp Physiol 59:223–239
Siebrasse JP, Kaminski T, Kubitscheck U (2012) Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy. Proc Natl Acad Sci USA 109:9426–9431
Silva Cd, Walter NG (2009) Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. RNA 15:76–84
Singh J, Padgett RA (2009) Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 16:1128–1133
Song WJ, Strack RL, Jaffrey SR (2013) Imaging bacterial protein expression using genetically encoded RNARNARNA sensors. Nat Methods 10:873
Strack RL, Disney MD, Jaffrey SR (2013) A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat Methods 10:1219
Stracy M, Uphoff S, Garza de Leon F, Kapanidis AN (2014) In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair. FEBS Lett. doi:10.1016/j.febslet.2014.05.026
Strulson CA, Molden RC, Keating CD, Bevilacqua PC (2012) RNA catalysis through compartmentalization. Nat Chem 4:941–946
Suddala KC et al (2013) Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res 41:10462–10475
Suzuki Y, Endo M, Yang Y, Sugiyama H (2014) Dynamic assembly/disassembly processes of photoresponsive DNA origami nanostructures directly visualized on a lipid membrane surface. J Am Chem Soc 136:1714–1717
Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, Puglisi JD (2010) Real-time tRNA transit on single translating ribosomes at condon resolution. Nature 464:1012–1017
van Kouwenhove M, Kedde M, Agami R (2011) MicroRNA regulation by RNA-binding proteins and its implications for cancer. Nat Rev Cancer 11:644–656
Vargas DY et al (2011) Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147:1054–1065
Waks Z, Klein AM, Silver PA (2011) Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol 7:506
Walter NG, Perumal S (2009) The small ribozymes: common and diverse features observed through the FRET lens. In: Walter NG, Woodson SA, Batey RT (eds) Non-protein coding RNAs. Springer, Heidelberg, pp 103–127
Walter NG, Huang C, Manzo AJ, Sobhy MA (2008) Do-it-yourself guide: how to use the modern single-molecule toolkit. Nat Methods 5:475–489
Wang S, Moffitt JR, Dempsey GT, Xie XS, Zhuang X (2014) Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging. Proc Natl Acad Sci USA 111:8452–8457
Wickham SFJ, Endo M, Katsuda Y, Hidaka K, Bath J, Sugiyama H, Turberfield AJ (2011) Direct observation of stepwise movement of a synthetic molecular transporter. Nat Nanotechnol 6:166–169
Wildenberg SMvd, Prevo B, Peterman EL (2011) A brief introduction to single-molecule fluorescence methods. Methods Mol Biol 783:81–99
Xia T, Li N, Fang X (2013) Single-molecule fluorescence imaging in living cells. Annu Rev Phys Chem 64:459–480
Xie XS, Yu J, Yang WY (2006) Living cells as test tubes. Science 312:228–230
Xu K, Zhong G, Zhuang X (2013) Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339:452–456
Yuan L, Lin W, Zheng K, He L, Huang W (2013) Far-red to near infrared analyte-responsive fluorescent probes based on organic fluorophore platforms for fluorescence imaging. Chem Soc Rev 42:622–661
Zhang DY, Seelig G (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem 3:103–113
Zhao R, Marshall M, Alemán EA, Lamichhane R, Feig A, Rueda D (2010) Laser-assisted single-molecule refolding (LASR). Biophys J 99:1925–1931
Zhou X, Choudhary E, Andoy NM, Zou N, Chen P (2013) Scalable parallel screening of catalyst activity at the single-particle level and subdiffraction resolution. ACS Catal 3:1448–1453
Zhuang X, Kim H, Pereira MJB, Babcock HP, Walter NG, Chu S (2002) Correlating structural dynamics and function in single ribozyme molecules. Science 296:1473–1476
Acknowledgments
This work was supported in part by National Institutes of Health Grants R01 GM062357, R01 GM098023 and R21 AI109791, and by the Department of Defense MURI Award W911NF-12-1-0420 to N.G.W.
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Widom, J.R., Dhakal, S., Heinicke, L.A. et al. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Arch Toxicol 88, 1965–1985 (2014). https://doi.org/10.1007/s00204-014-1357-9
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DOI: https://doi.org/10.1007/s00204-014-1357-9