Photostable and photoswitching fluorescent dyes for super-resolution imaging

  • Masafumi Minoshima
  • Kazuya Kikuchi
Part of the following topical collections:
  1. AsBIC8: 8th Asian Biological Inorganic Chemistry Special Issue


Super-resolution fluorescence microscopy is a recently developed imaging tool for biological researches. Several methods have been developed for detection of fluorescence signals from molecules in a subdiffraction-limited area, breaking the diffraction limit of the conventional optical microscopies and allowing visualization of detailed macromolecular structures in cells. As objectives are exposed to intense laser in the optical systems, fluorophores for super-resolution microscopy must be tolerated even under severe light irradiation conditions. The fluorophores must also be photoactivatable and photoswitchable for single-molecule localization-based super-resolution microscopy, because the number of active fluorophores must be controlled by light irradiation. This has led to growing interest in these properties in the development of fluorophores. In this mini-review, we focus on the development of photostable and photoswitching fluorescent dyes for super-resolution microscopy. We introduce recent efforts, including improvement of fluorophore photostability and control of photoswitching behaviors of fluorophores based on photochemical and photophysical processes. Understanding and manipulation of chemical reactions in excited fluorophores can develop highly photostable and efficiently photoswitchable fluorophores that are suitable for super-resolution imaging applications.


Super-resolution microscopy Fluorophores Photostability Photoactivation Photoswitching 



This work was supported by Grants-in-Aid for Scientific Research of JSPS (Grants 25220207, 26102529, 15K12754 to K.K., and 16K01933 to M.M.), CREST of JST (K.K.), Asahi Glass Foundation (K.K.), Uehara Memorial Foundation (K.K.).


  1. 1.
    Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA (2010) Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev 90:1103–1163PubMedCrossRefGoogle Scholar
  2. 2.
    Lavis LD, Raines RT (2014) Bright building blocks for chemical biology. ACS Chem Biol 9:855–866PubMedPubMedCentralCrossRefGoogle Scholar
  3. 3.
    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 307:538–544PubMedPubMedCentralCrossRefGoogle Scholar
  4. 4.
    Hell SW (2007) Far-field optical nanoscopy. Science 316:1153–1158PubMedCrossRefGoogle Scholar
  5. 5.
    Huang B, Babcock H, Zhuang X (2010) Breaking the diffraction barrier: super-resolution imaging of cells. Cell 143:1047–1058PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Abbe E (1873) Contributions to the understanding of microscope theory. Arch Mikrosk Anat 9:413–418CrossRefGoogle Scholar
  7. 7.
    Hell SW, Wichmann J (1994) Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt Lett 19:780–782PubMedCrossRefGoogle Scholar
  8. 8.
    Klar TA, Jakobs S, Dyba M, Egner A, Hell SW (2000) Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proc Natl Acad Sci USA 97:8206–8210PubMedPubMedCentralCrossRefGoogle Scholar
  9. 9.
    Hofmann M, Eggeling C, Jakobs S, Hell SW (2005) Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proc Natl Acad Sci USA 102:17565–17569PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Gustafsson MGL (2005) Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc Natl Acad Sci USA 102:13081–13086PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Willig KI, Rizzoli SO, Westphal V, Jahn R, Hell SW (2006) STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature 440:935–939PubMedCrossRefGoogle Scholar
  12. 12.
    Willig KI, Kellner R, Medda R, Hein B, Jakobs S, Hell SW (2006) Nanoscale resolution in GFP-based microscopy. Nat Methods 3:721–723PubMedCrossRefGoogle Scholar
  13. 13.
    Donnert G, Keller J, Medda R, Andrei MA, Rizzoli SO, Lührmann R, Jahn R, Eggeling C, Hell SW (2006) Macromolecular-scale resolution in biological fluorescence microscopy. Proc Natl Acad Sci USA 103:11440–11445PubMedPubMedCentralCrossRefGoogle Scholar
  14. 14.
    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 457:1159–1162PubMedCrossRefGoogle Scholar
  15. 15.
    Westphal V, Rizzoli SO, Lauterbach MA, Kamin D, Jahn R, Hell SW (2008) Video-rate far-field optical nanoscopy dissects synaptic vesicle movement. Science 320:246–249PubMedCrossRefGoogle Scholar
  16. 16.
    Nägerl UV, Willig KI, Hein B, Hell SW, Bonhoeffer T (2008) Live-cell imaging of dendritic spines by STED microscopy. Proc Natl Acad Sci USA 105:18982–18987PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Schneider J, Zahn J, Maglione M, Sigrist SJ, Marquard J, Chojnacki, Kräusslich H-G, Sahl SJ, Engelhardt J, Hell SW (2015) Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics. Nat Methods 12:827–830PubMedCrossRefGoogle Scholar
  18. 18.
    Berning S, Willig KI, Steffens H, Dibaj P, Hell SW (2012) Nanoscopy in a living mouse brain. Science 335:551PubMedCrossRefGoogle Scholar
  19. 19.
    Gustaffson MGL (2000) Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J Microsc 198:82–87CrossRefGoogle Scholar
  20. 20.
    Schermelleh L, Carlton P, Haase S, Shao L, Winoto L, Kner P, Burke B, Cardoso CM, Agard DA, Gustafsson MGL, Leonhardt H, Sedat JW (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320:1332–1336PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Kner P, Chhun B, Griffis E, Winoto L, Gustafsson MGL (2009) Super-resolution video microscopy of live cells by structured illumination. Nat Methods 6:339–342PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolutio. Science 313:1642–1645PubMedCrossRefGoogle Scholar
  23. 23.
    Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–795PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Betzig E, Trautman JK, Harris TD, Weiner JS, Kostelak RL (1991) Breaking the diffraction barrier-optical microscopy on a nanometric scale. Science 251:1468–1470PubMedCrossRefGoogle Scholar
  25. 25.
    Axelrod D (1981) Cell-substrate contacts illuminated by total internal reflection fluorescence. J Cell Biol 89:141–145PubMedCrossRefGoogle Scholar
  26. 26.
    Moerner WE (2006) Single-molecule mountains yield nanoscale cell images. Nat Methods 3:781–782PubMedPubMedCentralCrossRefGoogle Scholar
  27. 27.
    Shroff H, Galbraith CG, Galbraith JA, Betzig E (2008) Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat Methods 5:417–423PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Shim S-H, Xia C, Zhong G, Babcock HP, Vaughan JC, Huang B, Wnag X, Xu C, Bi G-Q, Zhuang X (2012) Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes. Proc Acad Natl Sci USA 109:13978–13983CrossRefGoogle Scholar
  29. 29.
    Kanchanawong P, Shtengel G, Pasapera A, Ramko E, Davidson M, Hess H, Waterman CM (2010) Nanoscale architecture of integrin-based cell adhesions. Nature 468:580–584PubMedPubMedCentralCrossRefGoogle Scholar
  30. 30.
    Bates M, Huang B, Dempsey GT, Zhuang X (2007) Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317:1749–1753PubMedPubMedCentralCrossRefGoogle Scholar
  31. 31.
    Xu K, Zhong G, Zhuang X (2013) Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339:452–456PubMedCrossRefGoogle Scholar
  32. 32.
    Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X (2015) Spatially resolved, highly multiplexed RNA profiling in single cell. Science 348:aaa6090PubMedPubMedCentralCrossRefGoogle Scholar
  33. 33.
    Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X (2016) Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529(418):422Google Scholar
  34. 34.
    Jones SA, Shim S-H, He J, Zhuang X (2011) Fast, three-dimensional super-resolution imaging of live cells. Nat Methods 6:499–505CrossRefGoogle Scholar
  35. 35.
    Hein B, Willig KI, Hell SW (2008) Stimulated emission depletion (STED) nanoscopy of a fluorescent protein-labeled organelle inside a living cell. Proc Natl Acad Sci USA 105:14271–14276PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Kasche V, Lindqvist L (1964) Reactions between the triplet state of fluorescein and oxygen. J Phys Chem 68:817–823CrossRefGoogle Scholar
  37. 37.
    Eggeling C, Widengren J, Rigler R, Seidel CAM (1998) Photobleaching of fluorescent dyes under conditions used for single-molecule detection: evidence of two-step photolysis. Anal Chem 70:2651–2659PubMedCrossRefGoogle Scholar
  38. 38.
    Benesch RE, Benesch R (1953) Enzymatic removal of oxygen for polarography and related methods. Science 118:447–448PubMedCrossRefGoogle Scholar
  39. 39.
    Mohanty J, Nau WM (2005) Host-guest complexation of neutral red with macrocyclic host molecules: Contrasting pKa shifts and binding affinities for cucurbit[7]uril and β-cyclodextrin. Angew Chem Int Ed 117:3816–3820CrossRefGoogle Scholar
  40. 40.
    Martyn TA, Moor JL, Halterman RL, Yip WT (2007) Cucurbit[7]uril induces superior probe performance for single-molecule detection. J Am Chem Soc 129:10338–10339PubMedCrossRefGoogle Scholar
  41. 41.
    Yau CM, Pascu SI, Odom SA, Warren JE, Klotz EJ, Frampton MJ, Williams CC, Coropceanu V, Kuimova MK, Phillips D, Barlow S, Brédas JL, Marder SR, Millar V, Anderson HL (2008) Stabilisation of a heptamethine cyanine dye by rotaxane encapsulation. Chem Commun (Camb) (25):2897–2899. doi: 10.1039/b802728e
  42. 42.
    Yang SK, Shi X, Park S, Ha T, Zimmerman SC (2013) A dendritic single-molecule fluorescent probe that is monovalent, photostable and minimally blinking. Nat Chem 5:692–697PubMedPubMedCentralCrossRefGoogle Scholar
  43. 43.
    Komatsu T, Oushiki D, Takeda A, Miyamura M, Ueno T, Terai T, Nagano T (2011) Rational design of boron dipyrromethene (BODIPY)-based photobleaching-resistant fluorophores applicable to a protein dynamics study. Chem Commun 47:10055–10057CrossRefGoogle Scholar
  44. 44.
    Toutchkine A, Nguyen D-V, Hahn KM (2007) Merocyanine dyes with improved photostability. Org Lett 9:2775–2777PubMedCrossRefGoogle Scholar
  45. 45.
    Renikuntla BR, Rose HC, Eldo J, Waggoner AS, Armitage BA (2004) Improved photostability and fluorescence properties through polyfluorination of a cyanine dye. Org Lett 6:909–912PubMedCrossRefGoogle Scholar
  46. 46.
    Panchuk-Voloshina N, Haugland RP, Bishop-Stewart J, Bhalgat MK, Millard PJ, Mao F, Leung W-Y, Haugland RP (1999) Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates. J Histochem Cytochem 47:1179–1188PubMedCrossRefGoogle Scholar
  47. 47.
    Grimm JB, English BP, Chen J, Slaughter JP, Zhang Z, Revyakin A, Patel R, Macklin JJ, Normanno D, Singer RH, Lionnet T, Lavis LD (2015) A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat Methods 12:244–250PubMedPubMedCentralCrossRefGoogle Scholar
  48. 48.
    Song X, Johnson A, Foley J (2008) 7-Azabicyclo [2.2.1] heptane as a unique and effective dialkylamino auxochrome moiety: demonstration in a fluorescent rhodamine dye. J Am Chem Soc 130:17652–17653PubMedCrossRefGoogle Scholar
  49. 49.
    Song L, Varma CAGO, Verhoeven JW, Tanke HJ (1996) Influence of the triplet excited state on the photobleaching kinetics of fluorescein in microscopy. Biophys J 70:2959–2968PubMedPubMedCentralCrossRefGoogle Scholar
  50. 50.
    Giloh H, Sedat JW (1982) Fluorescence microscopy: reduced photobleaching of rhodamine and fluorescein protein conjugates by n-propyl gallate. Science 217:1252–1255PubMedCrossRefGoogle Scholar
  51. 51.
    Widengren J, Chmyrov A, Eggeling C, Löfdahl PÅ, Seidel CA (2007) Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy. J Phys Chem A 111:429–440PubMedCrossRefGoogle Scholar
  52. 52.
    Rasnik I, McKinney SA, Ha T (2006) Nonblinking and long-lasting single-molecule fluorescence imaging. Nat Methods 3:891–893PubMedCrossRefGoogle Scholar
  53. 53.
    Cordes T, Vogelsang J, Tinnefeld P (2009) On the mechanism of Trolox as antiblinking and antibleaching reagent. J Am Chem Soc 131:5018–5019PubMedCrossRefGoogle Scholar
  54. 54.
    Vogelsang J, Kasper R, Steinhauer C, Person B, Heilemann M, Sauer M, Tinnefeld P (2008) A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes. Angew Chem Int Ed 47:5465–5469CrossRefGoogle Scholar
  55. 55.
    Adamczyk A, Wilkinson F (1972) Quenching of triplet states by Schiff base nickel (II) complexes. J Chem Soc, Faraday Trans 68:2031–2041CrossRefGoogle Scholar
  56. 56.
    Glembockyte V, Lincoln R, Cosa G (2015) Cy3 photoprotection mediated by Ni2+ for extended single-molecule imaging: old tricks for new techniques. J Am Chem Soc 137:1116–1122PubMedCrossRefGoogle Scholar
  57. 57.
    Altman RB, Terry DS, Zhou Z, Zheng Q, Geggier P, Kolster RA, Zhao Y, Javitch JA, Warren JD, Blanchard SC (2012) Cyanine fluorophore derivatives with enhanced photostability. Nat Methods 9:68–71CrossRefGoogle Scholar
  58. 58.
    Altman RB, Zheng Q, Zhou Z, Terry DS, Warren JD, Blanchard SC (2012) Enhanced photostability of cyanine fluorophores across the visible spectrum. Nat Methods 9:428–429PubMedPubMedCentralCrossRefGoogle Scholar
  59. 59.
    Tinnefeld P, Cordes T (2012) Self-healing’dyes: intramolecular stabilization of organic fluorophores. Nat Methods 9:426–427PubMedCrossRefGoogle Scholar
  60. 60.
    Zheng Q, Jockusch S, Zhou Z, Altman RB, Warren JD, Turro NJ, Blanchard SC (2012) On the mechanisms of cyanine fluorophore photostabilization. J Phys Chem Lett 3:2200–2203PubMedPubMedCentralCrossRefGoogle Scholar
  61. 61.
    van der Velde JHM, Oelerich J, Huang J, Smit JH, Jazi AA, Galiani S, Kolmakov K, Guoridis G, Eggeling C, Herrmann A, Roelfes G, Cordes T (2015) A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization. Nat Commun 7:10144CrossRefGoogle Scholar
  62. 62.
    Grotjohann T, Testa I, Leutenegger M, Bock H, Urban NT, Lavoie-Cardinal F, Willig KI, Eggeling C, Jakobs S, Hell SW (2011) Diffraction-unlimited all-optical imaging and writing with a photochromic GFP. Nature 478:204–208PubMedCrossRefGoogle Scholar
  63. 63.
    Brakemann T, Stiel AC, Weber G, Andresen M, Testa I, Grotjohann T, Leutenegger M, Plessmann U, Urlaub H, Eggeling C, Whal MC, Hell SW, Jakobs S (2011) A reversibly photoswitchable GFP-like protein with fluorescence excitation decoupled from switching. Nat Biotechnol 29:942–947PubMedCrossRefGoogle Scholar
  64. 64.
    Grotjohann T, Testa I, Reuss M, Brakemann T, Eggeling C, Hell SW, Jakobs S (2012) rsEGFP2 enables fast RESOLFT nanoscopy of living cells. eLife 1:e00248PubMedPubMedCentralCrossRefGoogle Scholar
  65. 65.
    Tiwari DK, Arai Y, Yamanaka M, Matsuda T, Agetsuma M, Nakano M, Fujita K, Nagai T (2015) A fast-and positively photoswitchable fluorescent protein for ultralow-laser-power RESOLFT nanoscopy. Nat Methods 12:515–518PubMedCrossRefGoogle Scholar
  66. 66.
    Adams SR, Tsien RY (1993) Controlling cell chemistry with caged compounds. Annu Rev Physiol 55:755–784PubMedCrossRefGoogle Scholar
  67. 67.
    Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J (2013) Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 113:119–191PubMedCrossRefGoogle Scholar
  68. 68.
    Mitchison TJ, Sawin KE, Theriot K, Mallavarapu GA (1998) Facile and general synthesis of photoactivatable xanthene dyes. Methods Enzymol 291:63–78PubMedCrossRefGoogle Scholar
  69. 69.
    Wysocki L, Grimm J, Tkachuk A, Brown T, Betzig E, Lavis L (2011) Facile and general synthesis of photoactivatable xanthene dyes. Angew Chem Int Ed 50:11206–11209CrossRefGoogle Scholar
  70. 70.
    Grimm J, Klein T, Kopek B, Shtengel G, Hess H, Sauer M, Lavis L, Grimm J, Klein T, Kopek B, Shtengel G, Hess H, Sauer M, Lavis L (2016) Synthesis of a Far-red photoactivatable silicon-containing rhodamine for super-resolution microscopy. Angew Chem Int Ed 55:1723–1727CrossRefGoogle Scholar
  71. 71.
    Belov VN, Wurm CA, Boyarskiy VP, Jakobs S, Hell SW (2010) Rhodamines NN: a novel class of caged fluorescent dyes. Angew Chem Int Ed 49:3520–3523CrossRefGoogle Scholar
  72. 72.
    Lord SJ, Conley NR, Lee HD, Samuel R, Liu N, Twieg RJ, Moerner WE (2008) A photoactivatable push–pull fluorophore for single-molecule imaging in live cells. J Am Chem Soc 130:9204–9205PubMedPubMedCentralCrossRefGoogle Scholar
  73. 73.
    Bates M, Blosser TR, Zhuang X (2005) Short-range spectroscopic ruler based on a single-molecule optical switch. Phys Rev Lett 94:108101PubMedPubMedCentralCrossRefGoogle Scholar
  74. 74.
    Heilemann M, van de Linde S, Schüttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P, Sauer M (2008) Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed 47:6172–6176CrossRefGoogle Scholar
  75. 75.
    Heilemann M, van de Linde S, Mukherjee A, Sauer M (2009) Super-resolution imaging with small organic fluorophores. Angew Chem Int Ed 48:6903–6908CrossRefGoogle Scholar
  76. 76.
    Vogelsang J, Cordes T, Forthmann C, Steinhauer C, Tinnefeld P (2009) Controlling the fluorescence of ordinary oxazine dyes for single-molecule switching and superresolution microscopy. Proc Natl Acad Sci USA 106:8107–8112PubMedPubMedCentralCrossRefGoogle Scholar
  77. 77.
    Dempsey GT, Bates M, Kowtoniuk WE, Liu DR, Tsien RY, Zhuang X (2009) Photoswitching mechanism of cyanine dyes. J Am Chem Soc 131:18192–18193PubMedPubMedCentralCrossRefGoogle Scholar
  78. 78.
    Heilemann M, Margeat E, Kasper R, Sauer M, Tinnefeld P (2005) Carbocyanine dyes as efficient reversible single-molecule optical switch. J Am Chem Soc 127:3801–3806PubMedCrossRefGoogle Scholar
  79. 79.
    Dempsey GT, Vaughan JC, Chen KH, Bates M, Zhuang X (2011) Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat Methods 8:1027–1036PubMedPubMedCentralCrossRefGoogle Scholar
  80. 80.
    Feringa BL, Browne WR (2011) Molecular switches, 2nd edn. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  81. 81.
    Bossi M, Belov V, Polyakova S, Hell SW (2006) Reversible red fluorescent molecular switches. Angew Chem Int Ed 45:7462–7465CrossRefGoogle Scholar
  82. 82.
    Fukaminato T, Doi T, Tamaoki N, Okuno K, Ishibashi Y, Miyasaka H, Irie M (2011) Single-molecule fluorescence photoswitching of a diarylethene-perylenebisimide dyad: non-destructive fluorescence readout. J Am Chem Soc 133:4984–4990PubMedCrossRefGoogle Scholar
  83. 83.
    Deniz E, Tomasulo M, Cusido J, Ylidiz I, Petriella M, Bossi ML, Sortino S, Raymo FM (2012) Photoactivatable fluorophores for super-resolution imaging based on oxazine auxochromes. J Phys Chem C 116:6058–6068CrossRefGoogle Scholar
  84. 84.
    Pang S-C, Hyun H, Lee S, Jang D, Lee MJ, Kang SH, Ahn K-H (2012) Photoswitchable fluorescent diarylethene in a turn-on mode for live cell imaging. Chem Commun 48:3745–3747CrossRefGoogle Scholar
  85. 85.
    Knauer KH, Gleiter R (1977) Photochromism of rhodamine derivatives. Angew Chem Int Ed 89:116–117CrossRefGoogle Scholar
  86. 86.
    Fölling J, Belov V, Kunetsky R, Medda R, Schönle A, Egner A, Eggeling C, Bossi M, Hell SW (2007) Photochromic rhodamines provide nanoscopy with optical sectioning. Angew Chem Int Ed 46:6266–6270CrossRefGoogle Scholar
  87. 87.
    Uno S, Kamiya M, Yoshihara T, Sugawara K, Okabe K, Tarhan MC, Fujita H, Funatsu T, Okada Y, Tobita S, Urano Y (2014) A spontaneously blinking fluorophore based on intramolecular spirocyclization for live-cell super-resolution imaging. Nat Chem 6:681–689PubMedGoogle Scholar
  88. 88.
    Sharonov A, Hochstrasser R (2006) Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proc Natl Acad Sci USA 103:18911–18916PubMedPubMedCentralCrossRefGoogle Scholar
  89. 89.
    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 11:313–318PubMedPubMedCentralCrossRefGoogle Scholar
  90. 90.
    Kiuchi T, Higuchi M, Takamura A, Maruoka M, Watanabe N (2015) Multitarget super-resolution microscopy with high-density labeling by exchangeable probes. Nat Methods 12:743–746PubMedCrossRefGoogle Scholar
  91. 91.
    Lukinavičius G, Reymond L, D’Este E, Masharina A, Göttfert F, Ta H, Güther A, Fournier M, Rizzo S, Waldmann H, Blaukopf C, Sommer C, Gerlich DW, Arndt H-D, Hell SW, Johnsson K (2014) Fluorogenic probes for live-cell imaging of the cytoskeleton. Nat Methods 731:11–733Google Scholar
  92. 92.
    Lukinavičius G, Blaukopf C, Pershagen E, Schena A, Reymond L, Derivery E, Gonzalez-Gaitan M, D’Este E, Hell SW, Gerlich DW, Johnsson K (2015) SiR-Hoechst is a far-red DNA stain for live-cell nanoscopy. Nature Commun 6:8497CrossRefGoogle Scholar
  93. 93.
    Best MD (2009) Click chemistry and bioorthogonal reactions: unprecedented selectivity in the labeling of biological molecules. Biochmistry 48:6571–6584CrossRefGoogle Scholar
  94. 94.
    Hao Z, Hong S, Chen X, Chen PR (2011) Introducing bioorthogonal functionalities into proteins in living cells. Acc Chem Res 44:742–751PubMedCrossRefGoogle Scholar
  95. 95.
    Zessin PJ, Finan K, Heilemann M (2012) Reversible fluorescence photoswitching in DNA. J Struct Biol 177:344–348PubMedCrossRefGoogle Scholar
  96. 96.
    Letschert S, Göhler A, Franke C, Bertleff-Zieschang N, Memmel E, Doose S, Seibel J, Sauer M (2014) Super-resolution imaging of plasma membrane glycans. Angew Chem Int Ed 53:10921–10924CrossRefGoogle Scholar
  97. 97.
    Nikić I, Plass T, Schraidt O, Szymański J, Briggs JA, Schultz C, Lemke EA (2014) Live-cell imaging of cyclopropene tags with fluorogenic tetrazine cycloadditions. Angew Chem Int Ed 53:2245–2249CrossRefGoogle Scholar
  98. 98.
    Uttamapinant C, Howe JD, Lang K, Beránek V, Davis L, Mahesh M, Barry NP, Chin JW (2015) Genetic code expansion enables live-cell and super-resolution imaging of site-specifically labeled cellular proteins. J Am Chem Soc 137:4602–4605PubMedPubMedCentralCrossRefGoogle Scholar
  99. 99.
    Griffin BA, Adams SR, Tsien RY (1998) Specific covalent labeling of recombinant protein molecules inside live cells. Science 281:269–272PubMedCrossRefGoogle Scholar
  100. 100.
    Los GV, Encell LP, McDougall MG, Hartzell DD, Karassina N, Zimprich C, Wood MG, Learish R, Ohana RF, Urh M, Simpson D, Mendez J, Zimmerman K, Otto P, Vidugiris G, Zhu J, Darzins A, Klaubert DH, Bulleit RF, Wood KV (2008) HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem Biol 3:373–382PubMedCrossRefGoogle Scholar
  101. 101.
    Keppler A, Gendreizig S, Gronemeyer T, Pick H, Vogel H, Johnsson K (2003) A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat Biotechnol 21:86–89PubMedCrossRefGoogle Scholar
  102. 102.
    Miller LW, Sable J, Goelet P, Sheetz MP, Cornish VW (2004) Methotrexate conjugates: a molecular in vivo protein tag. Angew Chem Int Ed 116:1704–1707CrossRefGoogle Scholar
  103. 103.
    Mizukami S, Watanabe S, Hori Y, Kikuchi K (2009) Covalent protein labeling based on noncatalytic β-lactamase and a designed FRET substrate. J Am Chem Soc 131:5016–5017PubMedCrossRefGoogle Scholar
  104. 104.
    Hori Y, Nakaki K, Sato M, Mizukami S, Kikuchi K (2012) Development of protein-labeling probes with a redesigned fluorogenic switch based on intramolecular association for no-wash live-cell imaging. Angew Chem Int Ed 51:5611–5614CrossRefGoogle Scholar
  105. 105.
    Szent-Gyorgyi C, Schmidt BF, Creeger Y, Fisher GW, Zakel KL, Adler S, Fitzpatrick AJ, Woolford CA, Yan Q, Vasilev KV, Berget PB, Bruchez MP, Jarvic JW, Waggoner A (2008) Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nat Biotechnol 26:235–240PubMedCrossRefGoogle Scholar
  106. 106.
    Chen I, Howarth M, Lin W, Ting AY (2005) Site-specific labeling of cell surface proteins with biophysical probes using biotin ligase. Nat Methods 2:99–104PubMedCrossRefGoogle Scholar
  107. 107.
    Lee HD, Lord SJ, Iwanaga S, Zhan K, Xie H, Williams JC, Wang H, Bowman GR, Goley ED, Shapiro L, Twieg RJ, Rao J, Moerner WE (2010) Superresolution imaging of targeted proteins in fixed and living cells using photoactivatable organic fluorophores. J Am Chem Soc 132:15099–15101PubMedPubMedCentralCrossRefGoogle Scholar
  108. 108.
    Lelek M, Di Nunzio F, Henriques R, Charneau P, Arhel N, Zimmer C (2012) Superresolution imaging of HIV in infected cells with FlAsH-PALM. Proc Natl Acad Sci USA 109:8564–8569PubMedPubMedCentralCrossRefGoogle Scholar
  109. 109.
    Wilmes S, Staufenbiel M, Liße D, Richter CP, Beutel O, Busch KB, Hess ST, Piehler J (2012) Triple-color super-resolution imaging of live cells: resolving submicroscopic receptor organization in the plasma membrane. Angew Chem Int Ed 51:4868–4871CrossRefGoogle Scholar
  110. 110.
    Lukinavičius G, Umezawa K, Olivier N, Honigmann A, Yang G, Plass T, Mueller V, Reymond L, Correa I Jr, Luo Z-G, Schultz C, Lemke EA, Heppenstall P, Eggeling C, Manley S, Johnsson K (2013) A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat Chem 5:132–139PubMedCrossRefGoogle Scholar
  111. 111.
    Wombacher R, Heidbreder M, van de Linde S, Sheetz MP, Heilemann M, Cornish VW, Sauer M (2010) Live-cell super-resolution imaging with trimethoprim conjugates. Nat Methods 7:717–719PubMedCrossRefGoogle Scholar
  112. 112.
    Fitzpatrick JAJ, Yan Q, Sieber JJ, Dyba M, Schwarz U, Szent-Gyorgyi C, Woolford CA, Berget PB, Waggoner AS, Bruchez MP (2009) STED nanoscopy in living cells using fluorogen activating proteins. Bioconjugate Chem 20:1843–1847CrossRefGoogle Scholar
  113. 113.
    Hama H, Kurokawa H, Kawano H, Ando R, Shimogori T, Noda H, Fukami K, Sakaue-Sawano A, Miyawaki A (2011) Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat Neurosci 14:1481–1488PubMedCrossRefGoogle Scholar
  114. 114.
    Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K (2013) Structural and molecular interrogation of intact biological systems. Nature 497:332–337PubMedPubMedCentralCrossRefGoogle Scholar
  115. 115.
    Susaki EA, Tainaka K, Perrin D, Kishino F, Tawara T, Watanabe TM, Yokoyama C, Onoe H, Eguchi M, Yamaguchi S, Abe T, Kiyonari H, Shimizu Y, Miyawaki A, Yokota H, Ueda HR (2014) Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157:726–739PubMedCrossRefGoogle Scholar
  116. 116.
    Chen F, Tillberg PW, Boyden ES (2015) Expansion microscopy. Science 347:543–548PubMedPubMedCentralCrossRefGoogle Scholar
  117. 117.
    Chozinski TJ, Halpern AR, Okawa H, Kim HJ, Tremel GJ, Wong RO, Vaughan JC (2016) Expansion microscopy with conventional antibodies and fluorescent proteins. Nat Methods 13:485–488PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© SBIC 2017

Authors and Affiliations

  1. 1.Graduate School of EngineeringOsaka UniversitySuitaJapan
  2. 2.Immunology Frontier Research Center (IFReC)Osaka UniversitySuitaJapan

Personalised recommendations