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Direct Stochastic Optical Reconstruction Microscopy (dSTORM)

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1251))

Abstract

Single-molecule localization-based super-resolution microscopy can be performed with regular, bright, and photostable organic fluorophores. We review a concept termed direct stochastic optical reconstruction microscopy (dSTORM), which operates conventional fluorophores as photoswitches and provides an optical resolution of ~20 nm. We introduce the principle of dSTORM, illustrate experimental schemes, and discuss approaches for data analysis.

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References

  1. Betzig E, Patterson GH, Sougrat R et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645

    Article  CAS  PubMed  Google Scholar 

  2. Heilemann M, van de Linde S, Schuttpelz M et al (2008) Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed Engl 47:6172–6176

    Article  CAS  PubMed  Google Scholar 

  3. Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–795

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. van de Linde S, Loschberger A, Klein T et al (2011) Direct stochastic optical reconstruction microscopy with standard fluorescent probes. Nat Protoc 6:991–1009

    Article  PubMed  Google Scholar 

  5. Bates M, Dempsey GT, Chen KH et al (2012) Multicolor super-resolution fluorescence imaging via multi-parameter fluorophore detection. ChemPhysChem 13:99–107

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Lampe A, Haucke V, Sigrist SJ et al (2012) Multi-colour direct STORM with red emitting carbocyanines. Biol Cell 104:229–237

    Article  CAS  PubMed  Google Scholar 

  7. van de Linde S, Endesfelder U, Mukherjee A et al (2009) Multicolor photoswitching microscopy for subdiffraction-resolution fluorescence imaging. Photochem Photobiol Sci 8:465–469

    Article  PubMed  Google Scholar 

  8. Endesfelder U, Malkusch S, Flottmann B et al (2011) Chemically induced photoswitching of fluorescent probes – a general concept for super-resolution microscopy. Molecules 16:3106–3118

    Article  CAS  PubMed  Google Scholar 

  9. Eckhardt M, Anders M, Muranyi W et al (2011) A SNAP-tagged derivative of HIV-1 – a versatile tool to study virus-cell interactions. PLoS One 6:e22007

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  10. Endesfelder U, van de Linde S, Wolter S et al (2010) Subdiffraction-resolution fluorescence microscopy of myosin-actin motility. ChemPhysChem 11:836–840

    Article  CAS  PubMed  Google Scholar 

  11. Wombacher R, Heidbreder M, van de Linde S et al (2010) Live-cell super-resolution imaging with trimethoprim conjugates. Nat Methods 7:717–719

    Article  CAS  PubMed  Google Scholar 

  12. van de Linde S, Heilemann M, Sauer M (2012) Live-cell super-resolution imaging with synthetic fluorophores. Annu Rev Phys Chem 63:519–540

    Article  PubMed  Google Scholar 

  13. Jones SA, Shim SH, He J et al (2011) Fast, three-dimensional super-resolution imaging of live cells. Nat Methods 8:499–508

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Nanguneri S, Flottmann B, Horstmann H et al (2012) Three-dimensional, tomographic super-resolution fluorescence imaging of serially sectioned thick samples. PLoS One 7:e38098

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Heilemann M, van de Linde S, Mukherjee A et al (2009) Super-resolution imaging with small organic fluorophores. Angew Chem Int Ed Engl 48:6903–6908

    Article  CAS  PubMed  Google Scholar 

  16. Miller LW, Cai Y, Sheetz MP et al (2005) In vivo protein labeling with trimethoprim conjugates: a flexible chemical tag. Nat Methods 2:255–257

    Article  CAS  PubMed  Google Scholar 

  17. Keppler A, Gendreizig S, Gronemeyer T et al (2003) A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat Biotechnol 21:86–89

    Article  CAS  PubMed  Google Scholar 

  18. Gautier A, Juillerat A, Heinis C et al (2008) An engineered protein tag for multiprotein labeling in living cells. Chem Biol 15:128–136

    Article  CAS  PubMed  Google Scholar 

  19. Los GV, Encell LP, McDougall MG et al (2008) HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem Biol 3:373–382

    Article  CAS  PubMed  Google Scholar 

  20. Salic A, Mitchison TJ (2008) A chemical method for fast and sensitive detection of DNA synthesis in vivo. Proc Natl Acad Sci U S A 105:2415–2420

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Besanceney-Webler C, Jiang H, Zheng T et al (2011) Increasing the efficacy of bioorthogonal click reactions for bioconjugation: a comparative study. Angew Chem Int Ed Engl 50:8051–8056

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. van de Linde S, Krstic I, Prisner T et al (2011) Photoinduced formation of reversible dye radicals and their impact on super-resolution imaging. Photochem Photobiol Sci 10:499–506

    Article  PubMed  Google Scholar 

  23. Kottke T, van de Linde S, Sauer M et al (2010) Identification of the product of photoswitching of an oxazine fluorophore using fourier transform infrared difference spectroscopy. J Phys Chem Lett 1:3156–3159

    Article  CAS  Google Scholar 

  24. Wolter S, Endesfelder U, van de Linde S et al (2011) Measuring localization performance of super-resolution algorithms on very active samples. Opt Express 19:7020–7033

    Article  PubMed  Google Scholar 

  25. Tokunaga M, Imamoto N, Sakata-Sogawa K (2008) Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat Methods 5:159–161

    Article  CAS  PubMed  Google Scholar 

  26. Wolter S, Sauer M (2012) Follow-up to paper by S. Wolter, M. Schuttpelz, M. Tscherepanow, S. van de Linde, M. Heilemann and M. Sauer, entitled Real-time computation of subdiffraction-resolution fluorescence images. J Microsc 245:109

    Article  CAS  PubMed  Google Scholar 

  27. Henriques R, Lelek M, Fornasiero EF et al (2010) QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. Nat Methods 7:339–340

    Article  CAS  PubMed  Google Scholar 

  28. Thompson RE, Larson DR, Webb WW (2002) Precise nanometer localization analysis for individual fluorescent probes. Biophys J 82:2775–2783

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  29. Mortensen KI, Churchman LS, Spudich JA et al (2010) Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat Methods 7:377–381

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Smith CS, Joseph N, Rieger B et al (2010) Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat Methods 7:373–375

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Baddeley D, Cannell MB, Soeller C (2010) Visualization of localization microscopy data. Microsc Microanal 16:64–72

    Article  CAS  PubMed  Google Scholar 

  32. Veatch SL, Machta BB, Shelby SA et al (2012) Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting. PLoS One 7:e31457

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  33. Annibale P, Vanni S, Scarselli M et al (2011) Quantitative photo activated localization microscopy: unraveling the effects of photoblinking. PLoS One 6:e22678

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Lando D, Endesfelder U, Berger H et al (2012) Quantitative single-molecule microscopy reveals that CENP-ACnp1 deposition occurs during G2 in fission yeast. Open Biol 2:120078

    Article  PubMed Central  PubMed  Google Scholar 

  35. Ripley BD (1977) Modelling spatial patterns. J R Stat Soc B 39:172–212

    Google Scholar 

  36. Bolte S, Cordelieres FP (2006) A guided tour into subcellular colocalization analysis in light microscopy. J Microsc 224:213–232

    Article  CAS  PubMed  Google Scholar 

  37. Zinchuk V, Zinchuk O (2008) Quantitative colocalization analysis of confocal fluorescence microscopy images. Curr Protoc Cell Biol, Unit 4.19

    Google Scholar 

  38. Malkusch S, Endesfelder U, Mondry J et al (2012) Coordinate-based colocalization analysis of single-molecule localization microscopy data. Histochem Cell Biol 137:1–10

    Article  CAS  PubMed  Google Scholar 

  39. Jones DP (2010) Redox sensing: orthogonal control in cell cycle and apoptosis signalling. J Intern Med 268:432–448

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  40. Huang B, Jones SA, Brandenburg B et al (2008) Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat Methods 5:1047–1052

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  41. Juette MF, Gould TJ, Lessard MD et al (2008) Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat Methods 5:527–529

    Article  CAS  PubMed  Google Scholar 

  42. Pavani SR, Thompson MA, Biteen JS et al (2009) Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function. Proc Natl Acad Sci U S A 106:2995–2999

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Cella ZF, Lavagnino Z, Perrone DM et al (2011) Live-cell 3D super-resolution imaging in thick biological samples. Nat Methods 8:1047–1049

    Article  Google Scholar 

  44. Rayleigh L (1896) On the theory of optical images, with special reference to the microscope. Philos Mag 42:167–195

    Article  Google Scholar 

  45. Huang B, Wang W, Bates M et al (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810–813

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  46. Shannon CE (1949) Communication in the presence of noise. Proc Inst Radio Eng 37:10–21

    Google Scholar 

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Acknowledgments

The authors thank Marina Dietz, Franziska Fricke, and Bianca Nouvertné for providing super-resolution images. This work was supported by the Bundesministerium für Bildung und Forschung (FORSYS program, grant number 0315262).

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Correspondence to Mike Heilemann .

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Endesfelder, U., Heilemann, M. (2015). Direct Stochastic Optical Reconstruction Microscopy (dSTORM). In: Verveer, P. (eds) Advanced Fluorescence Microscopy. Methods in Molecular Biology, vol 1251. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2080-8_14

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  • DOI: https://doi.org/10.1007/978-1-4939-2080-8_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2079-2

  • Online ISBN: 978-1-4939-2080-8

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