Abstract
In the past decades, single-molecule fluorescence (SMF) techniques have been booming as they provide researchers with valuable molecular information that are unobtainable by using ensemble techniques. Applications of SMF techniques to live cell membranes have revolutionized our views on many cellular processes. In this chapter, we describe the basics of SMF techniques such as SMF imaging, single-molecule fluorescence resonance energy transfer (sm-FRET), and fluorescence correlation spectroscopy (FCS) and then discuss their contributions to the understanding of live cell membranes. We finally provide the practical protocols of applying SMF techniques to live cell membranes, including the choice of fluorescent probes, labeling strategies, cell sample preparation, instrumentation setup, and data analysis.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Moerner WE, Kador L (1989) Optical detection and spectroscopy of single molecules in a solid. Phys Rev Lett 62(21):2535–2538
Orrit M, Bernard J (1990) Single pentacene molecules detected by fluorescence excitation in a p-terphenyl crystal. Phys Rev Lett 65(21):2716–2719
Betzig E, Chichester RJ (1993) Single molecules observed by near-field scanning optical microscopy. Science 262(5138):1422–1425
Funatsu T, Harada Y, Tokunaga M, Saito K, Yanagida T (1995) Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous solution. Nature 374(6522):555–559
Sako Y, Minoghchi S, Yanagida T (2000) Single-molecule imaging of EGFR signalling on the surface of living cells. Nat Cell Biol 2(3):168–172
Tokunaga M, Kitamura K, Saito K, Iwane AH, Yanagida T (1997) Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy. Biochem Biophys Res Commun 235(1):47–53
Axelrod D (2001) Selective imaging of surface fluorescence with very high aperture microscope objectives. J Biomed Opt 6(1):6–13
Axelrod D (1981) Cell-substrate contacts illuminated by total internal reflection fluorescence. J Cell Biol 89(1):141–145
Stout AL, Axelrod D (1989) Evanescent field excitation of fluorescence by epi-illumination microscopy. Appl Opt 28(24):5237–5242
Sako Y, Yanagida T (2003) Single-molecule visualization in cell biology. Nat Rev Mol Cell Biol:SS1–5
Schütz G, Schindler H, Schmidt T (1997) Single-molecule microscopy on model membranes reveals anomalous diffusion. Biophys J 73(2):1073–1080
Ide T, Yanagida T (1999) An artificial lipid bilayer formed on an agarose-coated glass for simultaneous electrical and optical measurement of single ion channels. Biochem Biophys Res Commun 265(2):595–599
Schmidt T, Schütz G, Baumgartner W, Gruber H, Schindler H (1996) Imaging of single molecule diffusion. Proc Natl Acad Sci U S A 93(7):2926–2929
Shen C, Knapp M, Puchinger MG, Shahzad A, Gaubitzer E, Shen AD, Koehler G (2014) Using fluorescence correlation spectroscopy (FCS) for IFN-g detection: a preliminary study. J Immunol Methods 407:35–39
Stryer L (1978) Fluorescence energy transfer as a spectroscopic ruler. Annu Rev Biochem 47(1):819–846
Weiss S (1999) Fluorescence spectroscopy of single biomolecules. Science 283(5408):1676–1683
Ishii Y, Yoshida T, Funatsu T, Wazawa T, Yanagida T (1999) Fluorescence resonance energy transfer between single fluorophores attached to a coiled-coil protein in aqueous solution. Chem Phys 247(1):163–173
Ha T, Enderle T, Ogletree D, Chemla D, Selvin P, 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(13):6264–6268
Padilla-Parra S, Tramier M (2012) FRET microscopy in the living cell: different approaches, strengths and weaknesses. Bioessays 34(5):369–376
Truong K, Ikura M (2001) The use of FRET imaging microscopy to detect protein–protein interactions and protein conformational changes in vivo. Curr Opin Struct Biol 11(5):573–578
Magde D, Elson E, Webb WW (1972) Thermodynamic fluctuations in a reacting system—measurement by fluorescence correlation spectroscopy. Phys Rev Lett 29(11):705–708
Elson EL, Magde D (1974) Fluorescence correlation spectroscopy. I. Conceptual basis and theory. Biopolymers 13(1):1–27
Magde D, Elson EL, Webb WW (1974) Fluorescence correlation spectroscopy. II. An experimental realization. Biopolymers 13(1):29–61
Webb WW (1976) Applications of fluorescence correlation spectroscopy. Q Rev Biophys 9(01):49–68
Chen H, Farkas ER, Webb WW (2008) In vivo applications of fluorescence correlation spectroscopy. Methods Cell Biol 89:3–35
Haustein E, Schwille P (2007) Fluorescence correlation spectroscopy: novel variations of an established technique. Annu Rev Biophys Biomol Struct 36:151–169
Eigen M, Rigler R (1994) Sorting single molecules: application to diagnostics and evolutionary biotechnology. Proc Natl Acad Sci U S A 91(13):5740–5747
Rauer B, Neumann E, Widengren J, Rigler R (1996) Fluorescence correlation spectrometry of the interaction kinetics of tetramethylrhodamin α-bungarotoxin with Torpedo californica acetylcholine receptor. Biophys Chem 58(1):3–12
Haupts U, Maiti S, Schwille P, Webb WW (1998) Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy. Proc Natl Acad Sci U S A 95(23):13573–13578
Schwille P, Haupts U, Maiti S, Webb WW (1999) Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one-and two-photon excitation. Biophys J 77(4):2251–2265
Singh AP, Wohland T (2014) Applications of imaging fluorescence correlation spectroscopy. Curr Opin Chem Biol 20:29–35
García-Sáez AJ, Schwille P (2007) Single molecule techniques for the study of membrane proteins. Appl Microbiol Biotechnol 76(2):257–266
García-Sáez AJ, Schwille P (2008) Fluorescence correlation spectroscopy for the study of membrane dynamics and protein/lipid interactions. Methods 46(2):116–122
Dertinger T, Pacheco V, von der Hocht I, Hartmann R, Gregor I, Enderlein J (2007) Two-focus fluorescence correlation spectroscopy: a new tool for accurate and absolute diffusion measurements. Chem Phys Chem 8(3):433–443
Schwille P (2001) Fluorescence correlation spectroscopy and its potential for intracellular applications. Cell Biochem Biophys 34(3):383–408
Fahey P, Koppel D, Barak L, Wolf D, Elson E, Webb W (1977) Lateral diffusion in planar lipid bilayers. Science 195(4275):305–306
Schwille P, Korlach J, Webb WW (1999) Fluorescence correlation spectroscopy with single-molecule sensitivity on cell and model membranes. Cytometry 36(3):176–182
Schlessinger J, Koppel D, Axelrod D, Jacobson K, Webb W, Elson E (1976) Lateral transport on cell membranes: mobility of concanavalin A receptors on myoblasts. Proc Natl Acad Sci U S A 73(7):2409–2413
Kahya N (2006) Targeting membrane proteins to liquid-ordered phases: molecular self-organization explored by fluorescence correlation spectroscopy. Chem Phys Lipids 141(1):158–168
Benda A, Beneš M, Marecek V, Lhotský A, Hermens WT, Hof M (2003) How to determine diffusion coefficients in planar phospholipid systems by confocal fluorescence correlation spectroscopy. Langmuir 19(10):4120–4126
Schwille P, Meyer-Almes F-J, Rigler R (1997) Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution. Biophys J 72(4):1878–1886
Bacia K, Kim SA, Schwille P (2006) Fluorescence cross-correlation spectroscopy in living cells. Nat Methods 3(2):83–89
Haustein E, Schwille P (2004) Single-molecule spectroscopic methods. Curr Opin Struct Biol 14(5):531–540
Lillemeier BF, Mörtelmaier MA, Forstner MB, Huppa JB, Groves JT, Davis MM (2010) TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation. Nat Immunol 11(1):90–96
Larson DR, Gosse JA, Holowka DA, Baird BA, Webb WW (2005) Temporally resolved interactions between antigen-stimulated IgE receptors and Lyn kinase on living cells. J Cell Biol 171(3):527–536
Xie XS, Yu J, Yang WY (2006) Living cells as test tubes. Science 312(5771):228–230
Teramura Y, Ichinose J, Takagi H, Nishida K, Yanagida T, Sako Y (2006) Single-molecule analysis of epidermal growth factor binding on the surface of living cells. EMBO J 25(18):4215–4222
Nguyen AH, Nguyen VT, Kamio Y, Higuchi H (2006) Single-molecule visualization of environment-sensitive fluorophores inserted into cell membranes by staphylococcal γ-hemolysin. Biochemistry 45(8):2570–2576
Uyemura T, Takagi H, Yanagida T, Sako Y (2005) Single-molecule analysis of epidermal growth factor signaling that leads to ultrasensitive calcium response. Biophys J 88(5):3720–3730
Tani T, Miyamoto Y, Fujimori KE, Taguchi T, Yanagida T, Sako Y, Harada Y (2005) Trafficking of a ligand-receptor complex on the growth cones as an essential step for the uptake of nerve growth factor at the distal end of the axon: a single-molecule analysis. J Neurosci 25(9):2181–2191
Ulbrich MH, Isacoff EY (2007) Subunit counting in membrane-bound proteins. Nat Methods 4(4):319–321
Iino R, Koyama I, Kusumi A (2001) Single molecule imaging of green fluorescent proteins in living cells: E-cadherin forms oligomers on the free cell surface. Biophys J 80(6):2667–2677
Harms GS, Cognet L, Lommerse PH, Blab GA, Kahr H, Gamsjäger R, Spaink HP, Soldatov NM, Romanin C, Schmidt T (2001) Single-molecule imaging of L-type Ca2+ channels in live cells. Biophys J 81(5):2639–2646
Murakoshi H, Iino R, Kobayashi T, Fujiwara T, Ohshima C, Yoshimura A, Kusumi A (2004) Single-molecule imaging analysis of Ras activation in living cells. Proc Natl Acad Sci U S A 101(19):7317–7322
Zhang W, Jiang Y, Wang Q, Ma X, Xiao Z, Zuo W, Fang X, Chen Y-G (2009) Single-molecule imaging reveals transforming growth factor-β-induced type II receptor dimerization. Proc Natl Acad Sci U S A 106(37):15679–15683
Maurice P, Kamal M, Jockers R (2011) Asymmetry of GPCR oligomers supports their functional relevance. Trends Pharmacol Sci 32(9):514–520
James JR, Oliveira MI, Carmo AM, Iaboni A, Davis SJ (2006) A rigorous experimental framework for detecting protein oligomerization using bioluminescence resonance energy transfer. Nat Methods 3(12):1001–1006
Meyer BH, Segura J-M, Martinez KL, Hovius R, George N, Johnsson K, Vogel H (2006) FRET imaging reveals that functional neurokinin-1 receptors are monomeric and reside in membrane microdomains of live cells. Proc Natl Acad Sci U S A 103(7):2138–2143
Kasai RS, Suzuki KG, Prossnitz ER, Koyama-Honda I, Nakada C, Fujiwara TK, Kusumi A (2011) Full characterization of GPCR monomer–dimer dynamic equilibrium by single molecule imaging. J Cell Biol 192(3):463–480
Hern JA, Baig AH, Mashanov GI, Birdsall B, Corrie JE, Lazareno S, Molloy JE, Birdsall NJ (2010) Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules. Proc Natl Acad Sci U S A 107(6):2693–2698
Calebiro D, Rieken F, Wagner J, Sungkaworn T, Zabel U, Borzi A, Cocucci E, Zürn A, Lohse MJ (2013) Single-molecule analysis of fluorescently labeled G-protein–coupled receptors reveals complexes with distinct dynamics and organization. Proc Natl Acad Sci U S A 110(2):743–748
Kusumi A, Tsunoyama TA, Hirosawa KM, Kasai RS, Fujiwara TK (2014) Tracking single molecules at work in living cells. Nat Chem Biol 10(7):524–532
Shibata SC, Hibino K, Mashimo T, Yanagida T, Sako Y (2006) Formation of signal transduction complexes during immobile phase of NGFR movements. Biochem Biophys Res Commun 342(1):316–322
Lommerse PH, Blab GA, Cognet L, Harms GS, Snaar-Jagalska BE, Spaink HP, Schmidt T (2004) Single-molecule imaging of the H-Ras membrane-anchor reveals domains in the cytoplasmic leaflet of the cell membrane. Biophys J 86(1):609–616
Ueda M, Sako Y, Tanaka T, Devreotes P, Yanagida T (2001) Single-molecule analysis of chemotactic signaling in Dictyostelium cells. Science 294(5543):864–867
Vrljic M, Nishimura SY, Brasselet S, Moerner W, McConnell HM (2002) Translational diffusion of individual Class II MHC membrane proteins in cells. Biophys J 83(5):2681–2692
Dahan M, Levi S, Luccardini C, Rostaing P, Riveau B, Triller A (2003) Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking. Science 302(5644):442–445
Chung I, Akita R, Vandlen R, Toomre D, Schlessinger J, Mellman I (2010) Spatial control of EGF receptor activation by reversible dimerization on living cells. Nature 464(7289):783-U163
Low-Nam ST, Lidke KA, Cutler PJ, Roovers RC, en Henegouwen PMVB, Wilson BS, Lidke DS (2011) ErbB1 dimerization is promoted by domain co-confinement and stabilized by ligand binding. Nat Struct Mol Biol 18(11):1244–1249
Webb SE, Roberts SK, Needham SR, Tynan CJ, Rolfe DJ, Winn MD, Clarke DT, Barraclough R, Martin-Fernandez ML (2008) Single-molecule imaging and fluorescence lifetime imaging microscopy show different structures for high-and low-affinity epidermal growth factor receptors in A431 cells. Biophys J 94(3):803–819
Zhang D, Manna M, Wohland T, Kraut R (2009) Alternate raft pathways cooperate to mediate slow diffusion and efficient uptake of a sphingolipid tracer to degradative and recycling compartments. J Cell Sci 122(20):3715–3728
Gerken M, Krippner-Heidenreich A, Steinert S, Willi S, Neugart F, Zappe A, Wrachtrup J, Tietz C, Scheurich P (2010) Fluorescence correlation spectroscopy reveals topological segregation of the two tumor necrosis factor membrane receptors. Biochim Biophys Acta 1798(6):1081–1089
Hegener O, Jordan R, Häberlein H (2004) Dye-labeled benzodiazepines: development of small ligands for receptor binding studies using fluorescence correlation spectroscopy. J Med Chem 47(14):3600–3605
Meissner O, Häberlein H (2003) Lateral mobility and specific binding to GABAA receptors on hippocampal neurons monitored by fluorescence correlation spectroscopy. Biochemistry 42(6):1667–1672
Gakamsky DM, Luescher IF, Pramanik A, Kopito RB, Lemonnier F, Vogel H, Rigler R, Pecht I (2005) CD8 kinetically promotes ligand binding to the T-cell antigen receptor. Biophys J 89(3):2121–2133
Hao H, Fan L, Chen T, Li R, Li X, He Q, Botella MA, Lin J (2014) Clathrin and membrane microdomains cooperatively regulate RbohD dynamics and activity in Arabidopsis. Plant Cell 26(4):1729–1745
Li X, Xing J, Qiu Z, He Q, Lin J (2016) Quantification of Membrane protein dynamics and interactions in plant cells by fluorescence correlation spectroscopy. Mol Plant 9(9):1229–1239
Lenne PF, Wawrezinieck L, Conchonaud F, Wurtz O, Boned A, Guo XJ, Rigneault H, He HT, Marguet D (2006) Dynamic molecular confinement in the plasma membrane by microdomains and the cytoskeleton meshwork. EMBO J 25(14):3245–3256
Leutenegger M, Ringemann C, Lasser T, Hell SW, Eggeling C (2012) Fluorescence correlation spectroscopy with a total internal reflection fluorescence STED microscope (TIRF-STED-FCS). Opt Express 20(5):5243–5263
Fan L, Hao H, Xue Y, Zhang L, Song K, Ding Z, Botella MA, Wang H, Lin J (2013) Dynamic analysis of Arabidopsis AP2 σ subunit reveals a key role in clathrin-mediated endocytosis and plant development. Development 140(18):3826–3837
Sakon JJ, Weninger KR (2010) Detecting the conformation of individual proteins in live cells. Nat Methods 7(3):203–205
Owen DM, Williamson D, Rentero C, Gaus K (2009) Quantitative microscopy: protein dynamics and membrane organisation. Traffic 10(8):962–971
Demir F, Horntrich C, Blachutzik JO, Scherzer S, Reinders Y, Kierszniowska S, Schulze WX, Harms GS, Hedrich R, Geiger D (2013) Arabidopsis nanodomain-delimited ABA signaling pathway regulates the anion channel SLAH3. Proc Natl Acad Sci U S A 110(20):8296–8301
Schütz GJ, Kada G, Pastushenko VP, Schindler H (2000) Properties of lipid microdomains in a muscle cell membrane visualized by single molecule microscopy. EMBO J 19(5):892–901
Douglass AD, Vale RD (2005) Single-molecule microscopy reveals plasma membrane microdomains created by protein-protein networks that exclude or trap signaling molecules in T cells. Cell 121(6):937–950
Mueller V, Ringemann C, Honigmann A, Schwarzmann G, Medda R, Leutenegger M, Polyakova S, Belov V, Hell S, Eggeling C (2011) STED nanoscopy reveals molecular details of cholesterol-and cytoskeleton-modulated lipid interactions in living cells. Biophys J 101(7):1651–1660
Sezgin E, Levental I, Grzybek M, Schwarzmann G, Mueller V, Honigmann A, Belov VN, Eggeling C, Coskun Ü, Simons K (2012) Partitioning, diffusion, and ligand binding of raft lipid analogs in model and cellular plasma membranes. Biochim Biophys Acta 1818(7):1777–1784
Eggeling C, Ringemann C, Medda R, Schwarzmann G, Sandhoff K, Polyakova S, Belov VN, Hein B, von Middendorff C, Schönle A (2009) Direct observation of the nanoscale dynamics of membrane lipids in a living cell. Nature 457(7233):1159–1162
Shaner NC, Steinbach PA, Tsien RY (2005) A guide to choosing fluorescent proteins. Nat Methods 2(12):905–909
Giepmans BN, Adams SR, Ellisman MH, Tsien RY (2006) The fluorescent toolbox for assessing protein location and function. Science 312(5771):217–224
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(3):223–239
Tsien RY (1998) The green fluorescent protein. Annu Rev Biochem 67(1):509–544
Griesbeck O (2004) Fluorescent proteins as sensors for cellular functions. Curr Opin Neurobiol 14(5):636–641
Hibino K, Shibata T, Yanagida T, Sako Y (2009) A RasGTP-induced conformational change in C-RAF is essential for accurate molecular recognition. Biophys J 97(5):1277–1287
Elf J, Li GW, Xie XS (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316(5828):1191–1194
Zacharias DA, Violin JD, Newton AC, Tsien RY (2002) Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 296(5569):913–916
Resch-Genger U, Grabolle M, Cavaliere-Jaricot S, Nitschke R, Nann T (2008) Quantum dots versus organic dyes as fluorescent labels. Nat Methods 5(9):763–775
Jaiswal JK, Goldman ER, Mattoussi H, Simon SM (2004) Use of quantum dots for live cell imaging. Nat Methods 1(1):73–78
Jaiswal JK, Simon SM (2004) Potentials and pitfalls of fluorescent quantum dots for biological imaging. Trends Cell Biol 14(9):497–504
Pinaud F, Clarke S, Sittner A, Dahan M (2010) Probing cellular events, one quantum dot at a time. Nat Methods 7(4):275–285
Liu SL, Zhang ZL, Sun EZ, Peng J, Xie M, Tian ZQ, Lin Y, Pang DW (2011) Visualizing the endocytic and exocytic processes of wheat germ agglutinin by quantum dot-based single-particle tracking. Biomaterials 32(30):7616–7624
Alivisatos AP, Gu W, Larabell C (2005) Quantum dots as cellular probes. Annu Rev Biomed Eng 7:55–76
Medintz IL, Uyeda HT, Goldman ER, Mattoussi H (2005) Quantum dot bioconjugates for imaging, labelling and sensing. Nat Mater 4(6):435–446
Michalet X, Pinaud FF, Bentolila LA, Tsay JM, Doose S, Li JJ, Sundaresan G, Wu AM, Gambhir SS, Weiss S (2005) Quantum dots for live cells, in vivo imaging, and diagnostics. Science 307(5709):538–544
Jiang X, Zhu M, Narain R (2014) Quantum Dots Bioconjugates. In: Narain R (ed) Chemistry of bioconjugates: synthesis, characterization, and biomedical applications. Wiley, Hoboken, New Jersey, pp 315–326
Acknowledgements
This work was supported by the National Natural Science Foundation of China (No. 21573289) and the Natural Science Foundation of Shandong Province (No. ZR2014BM028).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
He, H., Wang, X., Huang, F. (2018). Analysis and Applications of Single-Molecule Fluorescence in Live Cell Membranes. In: Wang, H., Li, G. (eds) Membrane Biophysics. Springer, Singapore. https://doi.org/10.1007/978-981-10-6823-2_6
Download citation
DOI: https://doi.org/10.1007/978-981-10-6823-2_6
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-6822-5
Online ISBN: 978-981-10-6823-2
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)