Abstract

Most fluorescence microscopy experiments today require a multicolor-capable setup, e.g. to study the interaction between different proteins. Multicolor capabilities are also well desirable for superresolution images. However, especially for STED (Stimulated Emission Depletion) microscopy, which requires two laser lines for a single color, multicolor imaging is technically challenging. Here we present a straightforward, easy-to-implement method to extend a single-color fluorescence (STED) microscope to a multichannel microscope without the need of modifying the optical setup. Therefore, we use a labeling technique based on complementary DNA sequences: a single-stranded short DNA sequence is attached to each structure to be imaged, different colors for labeling different features are represented by different sequences. Within the imaging process, the corresponding complementary sequence labeled with an organic fluorophore is added and transiently binds to the corresponding structure. After imaging, the labeled sequence is washed away and replaced by a second fluorescently labeled DNA strand complementary to the sequence bound to another feature. This way, multiplexing is achieved using only one arbitrary fluorophore, therefore aberrations are avoided.

© 2015 Optical Society of America

Full Article  |  PDF Article
OSA Recommended Articles
Simultaneous multi-lifetime multi-color STED imaging for colocalization analyses

Johanna Bückers, Dominik Wildanger, Giuseppe Vicidomini, Lars Kastrup, and Stefan W. Hell
Opt. Express 19(4) 3130-3143 (2011)

Simultaneous dual-color 3D STED microscopy

Christian Osseforth, Jeffrey R. Moffitt, Lothar Schermelleh, and Jens Michaelis
Opt. Express 22(6) 7028-7039 (2014)

Two-color STED microscopy in living cells

Patrina A. Pellett, Xiaoli Sun, Travis J. Gould, James E. Rothman, Ming-Qun Xu, Ivan R. Corrêa, and Joerg Bewersdorf
Biomed. Opt. Express 2(8) 2364-2371 (2011)

References

  • View by:
  • |
  • |
  • |

  1. Nobelprize.org, http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2014/press.html , (2014), retrieved.
  2. S. W. Hell and J. Wichmann, “Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy,” Opt. Lett. 19(11), 780–782 (1994).
    [Crossref] [PubMed]
  3. T. A. Klar and S. W. Hell, “Subdiffraction resolution in far-field fluorescence microscopy,” Opt. Lett. 24(14), 954–956 (1999).
    [Crossref] [PubMed]
  4. T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
    [Crossref] [PubMed]
  5. M. Fernández-Suárez and A. Y. Ting, “Fluorescent probes for super-resolution imaging in living cells,” Nat. Rev. Mol. Cell Biol. 9(12), 929–943 (2008).
    [Crossref] [PubMed]
  6. S. W. Hell, “Microscopy and its focal switch,” Nat. Methods 6(1), 24–32 (2009).
    [Crossref] [PubMed]
  7. S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
    [Crossref] [PubMed]
  8. L. Schermelleh, R. Heintzmann, and H. Leonhardt, “A guide to super-resolution fluorescence microscopy,” J. Cell Biol. 190(2), 165–175 (2010).
    [Crossref] [PubMed]
  9. G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
    [Crossref] [PubMed]
  10. F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
    [Crossref] [PubMed]
  11. J. Bückers, D. Wildanger, G. Vicidomini, L. Kastrup, and S. W. Hell, “Simultaneous multi-lifetime multi-color STED imaging for colocalization analyses,” Opt. Express 19(4), 3130–3143 (2011).
    [Crossref] [PubMed]
  12. D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
    [Crossref] [PubMed]
  13. T. Cordes, J. Vogelsang, C. Steinhauer, I. Stein, C. Forthmann, A. Gietl, J. Schmied, G. Acuna, S. Laurien, B. Lalkens, and P. Tinnefeld, Far-Field Nanoscopy with Conventional Fluorophores: Photostability, Photophysics, and Transient Binding (Springer, 2012), pp. 1–28.
  14. R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
    [Crossref] [PubMed]
  15. A. Schonle, “Imsepctor Image Acquisition & Analysis Software, v0.10,” (2006).
  16. T. Cordes, J. Vogelsang, and P. Tinnefeld, “On the mechanism of Trolox as antiblinking and antibleaching reagent,” J. Am. Chem. Soc. 131(14), 5018–5019 (2009).
    [Crossref] [PubMed]
  17. P. W. Rothemund, “Folding DNA to create nanoscale shapes and patterns,” Nature 440(7082), 297–302 (2006).
    [Crossref] [PubMed]
  18. S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
    [Crossref] [PubMed]
  19. J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
    [Crossref] [PubMed]
  20. C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
    [Crossref] [PubMed]
  21. M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
    [Crossref] [PubMed]
  22. N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
    [Crossref] [PubMed]
  23. R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
    [Crossref] [PubMed]
  24. C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
    [Crossref] [PubMed]
  25. M. Ogawa, N. Kosaka, P. L. Choyke, and H. Kobayashi, “H-type dimer formation of fluorophores: A mechanism for activatable, in vivo optical molecular imaging,” ACS Chem. Biol. 4(7), 535–546 (2009).
    [Crossref] [PubMed]
  26. S. Woo and P. W. K. Rothemund, “Programmable molecular recognition based on the geometry of DNA nanostructures,” Nat. Chem. 3(8), 620–627 (2011).
    [Crossref] [PubMed]
  27. Z. Li, L. Wang, H. Yan, and Y. Liu, “Effect of DNA hairpin loops on the twist of planar DNA origami tiles,” Langmuir 28(4), 1959–1965 (2012).
    [Crossref] [PubMed]
  28. A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
    [Crossref] [PubMed]
  29. G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
    [Crossref] [PubMed]
  30. N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
    [Crossref] [PubMed]

2014 (5)

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
[Crossref] [PubMed]

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
[Crossref] [PubMed]

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

2013 (1)

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

2012 (3)

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Z. Li, L. Wang, H. Yan, and Y. Liu, “Effect of DNA hairpin loops on the twist of planar DNA origami tiles,” Langmuir 28(4), 1959–1965 (2012).
[Crossref] [PubMed]

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

2011 (2)

2010 (2)

L. Schermelleh, R. Heintzmann, and H. Leonhardt, “A guide to super-resolution fluorescence microscopy,” J. Cell Biol. 190(2), 165–175 (2010).
[Crossref] [PubMed]

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

2009 (4)

T. Cordes, J. Vogelsang, and P. Tinnefeld, “On the mechanism of Trolox as antiblinking and antibleaching reagent,” J. Am. Chem. Soc. 131(14), 5018–5019 (2009).
[Crossref] [PubMed]

C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
[Crossref] [PubMed]

M. Ogawa, N. Kosaka, P. L. Choyke, and H. Kobayashi, “H-type dimer formation of fluorophores: A mechanism for activatable, in vivo optical molecular imaging,” ACS Chem. Biol. 4(7), 535–546 (2009).
[Crossref] [PubMed]

S. W. Hell, “Microscopy and its focal switch,” Nat. Methods 6(1), 24–32 (2009).
[Crossref] [PubMed]

2008 (2)

M. Fernández-Suárez and A. Y. Ting, “Fluorescent probes for super-resolution imaging in living cells,” Nat. Rev. Mol. Cell Biol. 9(12), 929–943 (2008).
[Crossref] [PubMed]

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

2007 (2)

S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[Crossref] [PubMed]

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

2006 (1)

P. W. Rothemund, “Folding DNA to create nanoscale shapes and patterns,” Nature 440(7082), 297–302 (2006).
[Crossref] [PubMed]

2004 (1)

N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
[Crossref] [PubMed]

2002 (1)

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

2000 (1)

T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
[Crossref] [PubMed]

1999 (1)

1994 (1)

Auer, G.

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Avendaño, M. S.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

Beater, S.

S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
[Crossref] [PubMed]

Berning, S.

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

Bückers, J.

Bulleit, R. F.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Choyke, P. L.

M. Ogawa, N. Kosaka, P. L. Choyke, and H. Kobayashi, “H-type dimer formation of fluorophores: A mechanism for activatable, in vivo optical molecular imaging,” ACS Chem. Biol. 4(7), 535–546 (2009).
[Crossref] [PubMed]

Church, G. M.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Cordes, T.

T. Cordes, J. Vogelsang, and P. Tinnefeld, “On the mechanism of Trolox as antiblinking and antibleaching reagent,” J. Am. Chem. Soc. 131(14), 5018–5019 (2009).
[Crossref] [PubMed]

Cordes, V. C.

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

Dai, M.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

Dammeyer, T.

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

Darzins, A.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Derr, N. D.

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

Donnert, G.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Dyba, M.

T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
[Crossref] [PubMed]

Eggeling, C.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Egner, A.

T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
[Crossref] [PubMed]

Encell, L. P.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Eriksson Karlström, A.

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Fernández-Suárez, M.

M. Fernández-Suárez and A. Y. Ting, “Fluorescent probes for super-resolution imaging in living cells,” Nat. Rev. Mol. Cell Biol. 9(12), 929–943 (2008).
[Crossref] [PubMed]

Forthmann, C.

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
[Crossref] [PubMed]

Gad, A. K. B.

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Gendreizig, S.

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

George, N.

N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
[Crossref] [PubMed]

Goodman, B. S.

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

Göttfert, F.

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

Gronemeyer, T.

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

Hartzell, D. D.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Heintzmann, R.

L. Schermelleh, R. Heintzmann, and H. Leonhardt, “A guide to super-resolution fluorescence microscopy,” J. Cell Biol. 190(2), 165–175 (2010).
[Crossref] [PubMed]

Hell, S. W.

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

J. Bückers, D. Wildanger, G. Vicidomini, L. Kastrup, and S. W. Hell, “Simultaneous multi-lifetime multi-color STED imaging for colocalization analyses,” Opt. Express 19(4), 3130–3143 (2011).
[Crossref] [PubMed]

S. W. Hell, “Microscopy and its focal switch,” Nat. Methods 6(1), 24–32 (2009).
[Crossref] [PubMed]

S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[Crossref] [PubMed]

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
[Crossref] [PubMed]

T. A. Klar and S. W. Hell, “Subdiffraction resolution in far-field fluorescence microscopy,” Opt. Lett. 24(14), 954–956 (1999).
[Crossref] [PubMed]

S. W. Hell and J. Wichmann, “Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy,” Opt. Lett. 19(11), 780–782 (1994).
[Crossref] [PubMed]

Holzmeister, P.

S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
[Crossref] [PubMed]

Honigmann, A.

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

Jahn, R.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Jakobs, S.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
[Crossref] [PubMed]

Johnsson, K.

N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
[Crossref] [PubMed]

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

Johnsson, N.

N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
[Crossref] [PubMed]

Jungmann, R.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
[Crossref] [PubMed]

Jusuk, I.

M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
[Crossref] [PubMed]

Karassina, N.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Kastrup, L.

Keller, J.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Keppler, A.

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

Klar, T. A.

T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
[Crossref] [PubMed]

T. A. Klar and S. W. Hell, “Subdiffraction resolution in far-field fluorescence microscopy,” Opt. Lett. 24(14), 954–956 (1999).
[Crossref] [PubMed]

Klaubert, D. H.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Kobayashi, H.

M. Ogawa, N. Kosaka, P. L. Choyke, and H. Kobayashi, “H-type dimer formation of fluorophores: A mechanism for activatable, in vivo optical molecular imaging,” ACS Chem. Biol. 4(7), 535–546 (2009).
[Crossref] [PubMed]

Kosaka, N.

M. Ogawa, N. Kosaka, P. L. Choyke, and H. Kobayashi, “H-type dimer formation of fluorophores: A mechanism for activatable, in vivo optical molecular imaging,” ACS Chem. Biol. 4(7), 535–546 (2009).
[Crossref] [PubMed]

Kuzyk, A.

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

Lalkens, B.

S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
[Crossref] [PubMed]

Learish, R.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Leifer, A. M.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Leonhardt, H.

L. Schermelleh, R. Heintzmann, and H. Leonhardt, “A guide to super-resolution fluorescence microscopy,” J. Cell Biol. 190(2), 165–175 (2010).
[Crossref] [PubMed]

Leschziner, A. E.

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

Levner, D.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Li, C.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Li, Z.

Z. Li, L. Wang, H. Yan, and Y. Liu, “Effect of DNA hairpin loops on the twist of planar DNA origami tiles,” Langmuir 28(4), 1959–1965 (2012).
[Crossref] [PubMed]

Lin, C.

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Liu, Y.

Z. Li, L. Wang, H. Yan, and Y. Liu, “Effect of DNA hairpin loops on the twist of planar DNA origami tiles,” Langmuir 28(4), 1959–1965 (2012).
[Crossref] [PubMed]

Los, G. V.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

McDougall, M. G.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Mendez, J.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Mueller, V.

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

Ogawa, M.

M. Ogawa, N. Kosaka, P. L. Choyke, and H. Kobayashi, “H-type dimer formation of fluorophores: A mechanism for activatable, in vivo optical molecular imaging,” ACS Chem. Biol. 4(7), 535–546 (2009).
[Crossref] [PubMed]

Ohana, R. F.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Otto, P.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Perols, A.

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Pibiri, E.

S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
[Crossref] [PubMed]

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

Pick, H.

N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
[Crossref] [PubMed]

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

Raab, M.

M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
[Crossref] [PubMed]

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

Reck-Peterson, S. L.

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

Rizzoli, S. O.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Rönnlund, D.

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Rothemund, P. W.

P. W. Rothemund, “Folding DNA to create nanoscale shapes and patterns,” Nature 440(7082), 297–302 (2006).
[Crossref] [PubMed]

Rothemund, P. W. K.

S. Woo and P. W. K. Rothemund, “Programmable molecular recognition based on the geometry of DNA nanostructures,” Nat. Chem. 3(8), 620–627 (2011).
[Crossref] [PubMed]

Scheible, M.

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

Schermelleh, L.

L. Schermelleh, R. Heintzmann, and H. Leonhardt, “A guide to super-resolution fluorescence microscopy,” J. Cell Biol. 190(2), 165–175 (2010).
[Crossref] [PubMed]

Schmied, J. J.

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
[Crossref] [PubMed]

Schonle, A.

A. Schonle, “Imsepctor Image Acquisition & Analysis Software, v0.10,” (2006).

Schönle, A.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Shih, W. M.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Simmel, F. C.

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
[Crossref] [PubMed]

Simpson, D.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Sobey, T. L.

C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
[Crossref] [PubMed]

Steinhauer, C.

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
[Crossref] [PubMed]

Ting, A. Y.

M. Fernández-Suárez and A. Y. Ting, “Fluorescent probes for super-resolution imaging in living cells,” Nat. Rev. Mol. Cell Biol. 9(12), 929–943 (2008).
[Crossref] [PubMed]

Tinnefeld, P.

M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
[Crossref] [PubMed]

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
[Crossref] [PubMed]

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

T. Cordes, J. Vogelsang, and P. Tinnefeld, “On the mechanism of Trolox as antiblinking and antibleaching reagent,” J. Am. Chem. Soc. 131(14), 5018–5019 (2009).
[Crossref] [PubMed]

C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
[Crossref] [PubMed]

Urh, M.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Vicidomini, G.

Vidugiris, G.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Vogel, H.

N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
[Crossref] [PubMed]

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

Vogelsang, J.

T. Cordes, J. Vogelsang, and P. Tinnefeld, “On the mechanism of Trolox as antiblinking and antibleaching reagent,” J. Am. Chem. Soc. 131(14), 5018–5019 (2009).
[Crossref] [PubMed]

Wang, L.

Z. Li, L. Wang, H. Yan, and Y. Liu, “Effect of DNA hairpin loops on the twist of planar DNA origami tiles,” Langmuir 28(4), 1959–1965 (2012).
[Crossref] [PubMed]

Westphal, V.

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Wichmann, J.

Widengren, J.

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Wildanger, D.

Woehrstein, J. B.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

Woo, S.

S. Woo and P. W. K. Rothemund, “Programmable molecular recognition based on the geometry of DNA nanostructures,” Nat. Chem. 3(8), 620–627 (2011).
[Crossref] [PubMed]

Wood, K. V.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Wood, M. G.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Wünsch, B.

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

Wurm, C. A.

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

Xu, L.

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Yan, H.

Z. Li, L. Wang, H. Yan, and Y. Liu, “Effect of DNA hairpin loops on the twist of planar DNA origami tiles,” Langmuir 28(4), 1959–1965 (2012).
[Crossref] [PubMed]

Yin, P.

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Zhu, J.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Zimmerman, K.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

Zimprich, C.

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

ACS Chem. Biol. (2)

M. Ogawa, N. Kosaka, P. L. Choyke, and H. Kobayashi, “H-type dimer formation of fluorophores: A mechanism for activatable, in vivo optical molecular imaging,” ACS Chem. Biol. 4(7), 535–546 (2009).
[Crossref] [PubMed]

G. V. Los, L. P. Encell, M. G. McDougall, D. D. Hartzell, N. Karassina, C. Zimprich, M. G. Wood, R. Learish, R. F. Ohana, M. Urh, D. Simpson, J. Mendez, K. Zimmerman, P. Otto, G. Vidugiris, J. Zhu, A. Darzins, D. H. Klaubert, R. F. Bulleit, and K. V. Wood, “HaloTag: A novel protein labeling technology for cell imaging and protein analysis,” ACS Chem. Biol. 3(6), 373–382 (2008).
[Crossref] [PubMed]

ACS Nano (1)

D. Rönnlund, L. Xu, A. Perols, A. K. B. Gad, A. Eriksson Karlström, G. Auer, and J. Widengren, “Multicolor fluorescence nanoscopy by photobleaching: Concept, verification, and its application to resolve selective storage of proteins in platelets,” ACS Nano 8(5), 4358–4365 (2014).
[Crossref] [PubMed]

Angew. Chem. Int. Ed. Engl. (1)

C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA Origami as a nanoscopic ruler for super-resolution microscopy,” Angew. Chem. Int. Ed. Engl. 48(47), 8870–8873 (2009).
[Crossref] [PubMed]

Biophys. J. (2)

G. Donnert, J. Keller, C. A. Wurm, S. O. Rizzoli, V. Westphal, A. Schönle, R. Jahn, S. Jakobs, C. Eggeling, and S. W. Hell, “Two-color far-field fluorescence nanoscopy,” Biophys. J. 92(8), L67–L69 (2007).
[Crossref] [PubMed]

F. Göttfert, C. A. Wurm, V. Mueller, S. Berning, V. C. Cordes, A. Honigmann, and S. W. Hell, “Coaligned dual-channel STED nanoscopy and molecular diffusion analysis at 20 nm resolution,” Biophys. J. 105(1), L01–L03 (2013).
[Crossref] [PubMed]

ChemPhysChem (1)

M. Raab, J. J. Schmied, I. Jusuk, C. Forthmann, and P. Tinnefeld, “Fluorescence microscopy with 6 nm resolution on DNA origami,” ChemPhysChem 15(12), 2431–2435 (2014).
[Crossref] [PubMed]

J. Am. Chem. Soc. (2)

N. George, H. Pick, H. Vogel, N. Johnsson, and K. Johnsson, “Specific labeling of cell surface proteins with chemically diverse compounds,” J. Am. Chem. Soc. 126(29), 8896–8897 (2004).
[Crossref] [PubMed]

T. Cordes, J. Vogelsang, and P. Tinnefeld, “On the mechanism of Trolox as antiblinking and antibleaching reagent,” J. Am. Chem. Soc. 131(14), 5018–5019 (2009).
[Crossref] [PubMed]

J. Cell Biol. (1)

L. Schermelleh, R. Heintzmann, and H. Leonhardt, “A guide to super-resolution fluorescence microscopy,” J. Cell Biol. 190(2), 165–175 (2010).
[Crossref] [PubMed]

Langmuir (1)

Z. Li, L. Wang, H. Yan, and Y. Liu, “Effect of DNA hairpin loops on the twist of planar DNA origami tiles,” Langmuir 28(4), 1959–1965 (2012).
[Crossref] [PubMed]

Nano Lett. (1)

R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Lett. 10(11), 4756–4761 (2010).
[Crossref] [PubMed]

Nat. Biotechnol. (1)

A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson, “A general method for the covalent labeling of fusion proteins with small molecules in vivo,” Nat. Biotechnol. 21(1), 86–89 (2002).
[Crossref] [PubMed]

Nat. Chem. (2)

S. Woo and P. W. K. Rothemund, “Programmable molecular recognition based on the geometry of DNA nanostructures,” Nat. Chem. 3(8), 620–627 (2011).
[Crossref] [PubMed]

C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. Levner, G. M. Church, W. M. Shih, and P. Yin, “Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA,” Nat. Chem. 4(10), 832–839 (2012).
[Crossref] [PubMed]

Nat. Methods (2)

R. Jungmann, M. S. Avendaño, J. B. Woehrstein, M. Dai, W. M. Shih, and P. Yin, “Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT,” Nat. Methods 11(3), 313–318 (2014).
[Crossref] [PubMed]

S. W. Hell, “Microscopy and its focal switch,” Nat. Methods 6(1), 24–32 (2009).
[Crossref] [PubMed]

Nat. Protoc. (1)

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch, T. Dammeyer, and P. Tinnefeld, “DNA origami-based standards for quantitative fluorescence microscopy,” Nat. Protoc. 9(6), 1367–1391 (2014).
[Crossref] [PubMed]

Nat. Rev. Mol. Cell Biol. (1)

M. Fernández-Suárez and A. Y. Ting, “Fluorescent probes for super-resolution imaging in living cells,” Nat. Rev. Mol. Cell Biol. 9(12), 929–943 (2008).
[Crossref] [PubMed]

Nature (1)

P. W. Rothemund, “Folding DNA to create nanoscale shapes and patterns,” Nature 440(7082), 297–302 (2006).
[Crossref] [PubMed]

Opt. Express (1)

Opt. Lett. (2)

Phys. Chem. Chem. Phys. (1)

S. Beater, P. Holzmeister, E. Pibiri, B. Lalkens, and P. Tinnefeld, “Choosing dyes for cw-STED nanoscopy using self-assembled nanorulers,” Phys. Chem. Chem. Phys. 16(15), 6990–6996 (2014).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U.S.A. (1)

T. A. Klar, S. Jakobs, M. Dyba, A. Egner, and S. W. Hell, “Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission,” Proc. Natl. Acad. Sci. U.S.A. 97(15), 8206–8210 (2000).
[Crossref] [PubMed]

Science (2)

S. W. Hell, “Far-field optical nanoscopy,” Science 316(5828), 1153–1158 (2007).
[Crossref] [PubMed]

N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, and S. L. Reck-Peterson, “Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold,” Science 338(6107), 662–665 (2012).
[Crossref] [PubMed]

Other (3)

Nobelprize.org, http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2014/press.html , (2014), retrieved.

A. Schonle, “Imsepctor Image Acquisition & Analysis Software, v0.10,” (2006).

T. Cordes, J. Vogelsang, C. Steinhauer, I. Stein, C. Forthmann, A. Gietl, J. Schmied, G. Acuna, S. Laurien, B. Lalkens, and P. Tinnefeld, Far-Field Nanoscopy with Conventional Fluorophores: Photostability, Photophysics, and Transient Binding (Springer, 2012), pp. 1–28.

Cited By

OSA participates in Crossref's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (3)

Fig. 1
Fig. 1 a) Principle of DNA based transient binding for STED: The structure of interest (e.g. a 12HB) was equipped with 19 docking strands with the sequence 1 (red) at each end and with 19 docking strands with sequence 2 (green) in the middle of the 12HB. By adding imager 1 complementary to sequence 1, the marks at the ends are exclusively and transiently labeled and imaged. After washing, imager 2 complementary to sequence 2 was added and imaged likewise. b) Schematic superresolution images corresponding to the labeling steps as described in 1A and overlay (middle panel). c) Fluorescence emission spectra of imager strands labeled with two OregonGreen488 dyes before and after binding the complementary DNA. An approx. 5 fold fluorescence increase is observed as self-quenching is avoided after hybridization.
Fig. 2
Fig. 2 a) Confocal (top) and STED (bottom) images of 12HBs imaged as described in Fig. 1.The marks at the ends of the 12HB are shown in red (corresponding to sequence 1), the mark in the center is shown in green (corresponding to sequence 2). Imaging was performed using OregonGreen488. b) Magnified view of one of the structures: The upper panel shows the confocal image, which does not reveal any structural features. The STED image (lower panel) clearly reveals a red double spot and a green spot in between. c) The intensity profiles of the red and the green channel overlaid in the same fashion as the images. The two red marks exhibit distances of 65 and 85 nm from the green matching the designed distances of 75 and 75 nm within measurement uncertainty.
Fig. 3
Fig. 3 Rectangular DNA origamis were equipped with specific DNA docking strands in each of the four corners and then imaged sequentially with the complementary imager strands. a) Overlaid confocal scans show a high yield of 4fold labeled structures but no structure. b) Overlaid STED scans of the same region verify the rectangular design of the four-color labeled rectangular DNA origami. c) A zoom of one of the structures and the corresponding scheme of the design show that the structure is visualized as designed. d) Intensity profiles verify the expected distances between the corners of 73 nm (diagonals, red-white, green-blue), 57 nm (long sides, white-blue, green-red) and 47 nm (short sides, blue-red, white-green), respectively. The intensity profiles are color-coded according to their color in the image, the white channel is shown in black. Images were taken with a pixel size of 40 nm for the confocal and 20 nm for the STED images.

Tables (1)

Tables Icon

Table 1 Sequences used for fluorescence labeling (italic: spacer between DNA origami and docking strand; OG488: OregonGreen488, the fluorophore used in all experiments)

Metrics