Super-resolution microscopy with DNA-PAINT (original) (raw)

• Gustafsson, M.G.L. Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl. Acad. Sci. USA 102, 13081–13086 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Hell, S.W. & Wichmann, J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt. Lett. 19, 780–782 (1994).
  Article CAS PubMed Google Scholar
• Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).
  Article CAS PubMed Google Scholar
• Hess, S.T., Girirajan, T.P.K. & Mason, M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258–4272 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Rust, M.J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–795 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Heilemann, M. et al. Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew. Chem. Int. Ed. Engl. 47, 6172–6176 (2008).
  Article CAS PubMed Google Scholar
• Hell, S.W. Far-field optical nanoscopy. Science 316, 1153–1158 (2007).
  Article CAS PubMed Google Scholar
• Sengupta, P. et al. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat. Methods 8, 969–975 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Xu, K., Zhong, G. & Zhuang, X. Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339, 452–456 (2012).
  Article PubMed CAS Google Scholar
• Honigmann, A. et al. Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nat. Struct. Mol. Biol. 20, 679–686 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Li, D. et al. ADVANCED IMAGING. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science 349, aab3500 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Galiani, S. et al. Super-resolution microscopy reveals compartmentalization of peroxisomal membrane proteins. J. Biol. Chem. 291, 16948–16962 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Hell, S.W. et al. The 2015 super-resolution microscopy roadmap. J. Phys. D Appl. Phys. 48, 443001 (2015).
  Article CAS Google Scholar
• Huang, B., Bates, M. & Zhuang, X. Super-resolution fluorescence microscopy. Annu. Rev. Biochem. 78, 993–1016 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Lippincott-Schwartz, J., Jennifer, L.-S. & Patterson, G.H. Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging. Trends Cell Biol. 19, 555–565 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Nieuwenhuizen, R.P.J. et al. Measuring image resolution in optical nanoscopy. Nat. Methods 10, 557–562 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Sharonov, A. & Hochstrasser, R.M. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proc. Natl. Acad. Sci. USA 103, 18911–18916 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Giannone, G. et al. Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density. Biophys. J. 99, 1303–1310 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Jungmann, R. et al. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 10, 4756–4761 (2010).
  Article CAS PubMed Google Scholar
• Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313–318 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Iinuma, R. et al. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344, 65–69 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Jungmann, R. et al. Quantitative super-resolution imaging with qPAINT. Nat. Methods 13, 439–442 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Dai, M., Jungmann, R. & Yin, P. Optical imaging of individual biomolecules in densely packed clusters. Nat. Nanotechnol. 11, 798–807 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Schlichthaerle, T., Strauss, M.T., Schueder, F., Woehrstein, J.B. & Jungmann, R. DNA nanotechnology and fluorescence applications. Curr. Opin. Biotechnol. 39, 41–47 (2016).
  Article CAS PubMed Google Scholar
• Agasti, S. et al. DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging. Chem. Sci. (2017) http://dx.doi.org/10.1039/c6sc05420j.
• Rasnik, I., McKinney, S.A. & Ha, T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat. Methods 3, 891–893 (2006).
  Article CAS PubMed Google Scholar
• Aitken, C.E., Marshall, R.A. & Puglisi, J.D. An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys. J. 94, 1826–1835 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Ha, T. & Tinnefeld, P. Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annu. Rev. Phys. Chem. 63, 595–617 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Ries, J., Kaplan, C., Platonova, E., Eghlidi, H. & Ewers, H. A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nat. Methods 9, 582–584 (2012).
  Article CAS PubMed Google Scholar
• Opazo, F. et al. Aptamers as potential tools for super-resolution microscopy. Nat. Methods 9, 938–939 (2012).
  Article CAS PubMed Google Scholar
• Tokunaga, M., Imamoto, N. & Sakata-Sogawa, K. Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat. Methods 5, 159–161 (2008).
  Article CAS PubMed Google Scholar
• Legant, W.R. et al. High-density three-dimensional localization microscopy across large volumes. Nat. Methods 13, 359–365 (2016).
  Article PubMed PubMed Central CAS Google Scholar
• Rothemund, P.W.K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
  Article CAS PubMed Google Scholar
• Seeman, N.C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).
  Article CAS PubMed Google Scholar
• Seeman, N.C. An overview of structural DNA nanotechnology. Mol. Biotechnol. 37, 246–257 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Douglas, S.M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Benson, E. et al. DNA rendering of polyhedral meshes at the nanoscale. Nature 523, 441–444 (2015).
  Article CAS PubMed Google Scholar
• Kim, D.-N., Kilchherr, F., Dietz, H. & Bathe, M. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res. 40, 2862–2868 (2012).
  Article CAS PubMed Google Scholar
• Douglas, S.M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Martin, T.G. & Dietz, H. Magnesium-free self-assembly of multi-layer DNA objects. Nat. Commun. 3, 1103 (2012).
  Article PubMed CAS Google Scholar
• Sobczak, J.-P.J., Martin, T.G., Gerling, T. & Dietz, H. Rapid folding of DNA into nanoscale shapes at constant temperature. Science 338, 1458–1461 (2012).
  Article CAS PubMed Google Scholar
• Bellot, G., Gaëtan, B., McClintock, M.A., Chenxiang, L. & Shih, W.M. Recovery of intact DNA nanostructures after agarose gel–based separation. Nat. Methods 8, 192–194 (2011).
  Article CAS PubMed Google Scholar
• Lin, C., Perrault, S.D., Kwak, M., Graf, F. & Shih, W.M. Purification of DNA-origami nanostructures by rate-zonal centrifugation. Nucleic Acids Res. 41, e40 (2013).
  Article CAS PubMed Google Scholar
• Stahl, E., Martin, T.G., Praetorius, F. & Dietz, H. Facile and scalable preparation of pure and dense DNA origami solutions. Angew. Chem. Int. Ed. Engl. 53, 12735–12740 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Steinhauer, C., Jungmann, R., Sobey, T.L., Simmel, F.C. & Tinnefeld, P. DNA origami as a nanoscopic ruler for super-resolution microscopy. Angew. Chem. Int. Ed. Engl. 48, 8870–8873 (2009).
  Article CAS PubMed Google Scholar
• Schmied, J.J. et al. DNA origami–based standards for quantitative fluorescence microscopy. Nat. Protoc. 9, 1367–1391 (2014).
  Article CAS PubMed Google Scholar
• Dean, K.M. & Palmer, A.E. Advances in fluorescence labeling strategies for dynamic cellular imaging. Nat. Chem. Biol. 10, 512–523 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Dempsey, G.T., Vaughan, J.C., Chen, K.H., Bates, M. & Zhuang, X. Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat. Methods 8, 1027–1036 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Mikhaylova, M. et al. Resolving bundled microtubules using anti-tubulin nanobodies. Nat. Commun. 6, 7933 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Los, G.V. et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis. ACS Chem. Biol. 3, 373–382 (2008).
  Article CAS PubMed Google Scholar
• Keppler, A., Pick, H., Arrivoli, C., Vogel, H. & Johnsson, K. Labeling of fusion proteins with synthetic fluorophores in live cells. Proc. Natl. Acad. Sci. USA 101, 9955–9959 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, L., Xie, J. & Schultz, P.G. Expanding the genetic code. Annu. Rev. Biophys. Biomol. Struct. 35, 225–249 (2006).
  Article PubMed CAS Google Scholar
• Schweller, R.M. et al. Multiplexed in situ immunofluorescence using dynamic DNA complexes. Angew. Chem. Int. Ed. Engl. 51, 9292–9296 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Ullal, A.V. et al. Cancer cell profiling by barcoding allows multiplexed protein analysis in fine-needle aspirates. Sci. Transl. Med. 6, 219ra9 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Gong, H. et al. Simple method to prepare oligonucleotide-conjugated antibodies and its application in multiplex protein detection in single cells. Bioconjug. Chem. 27, 217–225 (2016).
  Article CAS PubMed Google Scholar
• Xu, K., Babcock, H.P. & Zhuang, X. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat. Methods 9, 185–188 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Whelan, D.R. & Bell, T.D.M. Image artifacts in single molecule localization microscopy: why optimization of sample preparation protocols matters. Sci. Rep. 5, 7924 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Edelstein, A.D. et al. J. Biol. Methods 1, 10 (2014).
  Article Google Scholar
• Beier, H.T. & Ibey, B.L. Experimental comparison of the high-speed imaging performance of an EM-CCD and sCMOS camera in a dynamic live-cell imaging test case. PLoS One 9, e84614 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Huang, F. et al. Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms. Nat. Methods 10, 653–658 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Shroff, H., Galbraith, C.G., Galbraith, J.A. & Betzig, E. Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics. Nat. Methods 5, 417–423 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Venkataramani, V., Herrmannsdörfer, F., Heilemann, M. & Kuner, T. SuReSim: simulating localization microscopy experiments from ground truth models. Nat. Methods 13, 319–321 (2016).
  Article PubMed CAS Google Scholar
• Sage, D. et al. Quantitative evaluation of software packages for single-molecule localization microscopy. Nat. Methods 12, 717–724 (2015).
  Article CAS PubMed Google Scholar
• Smith, C.S., Joseph, N., Rieger, B. & Lidke, K.A. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 7, 373–375 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Egner, A. et al. Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters. Biophys. J. 93, 3285–3290 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, Y. et al. Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm. Opt. Express 22, 15982–15991 (2014).
  Article PubMed PubMed Central Google Scholar
• Endesfelder, U., Malkusch, S., Fricke, F. & Heilemann, M. A simple method to estimate the average localization precision of a single-molecule localization microscopy experiment. Histochem. Cell Biol. 141, 629–638 (2014).
  Article CAS PubMed Google Scholar
• Lin, C. et al. Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat. Chem. 4, 832–839 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Bates, M., Huang, B., Dempsey, G.T. & Zhuang, X. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317, 1749–1753 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Huang, B., Jones, S.A., Brandenburg, B. & Zhuang, X. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat. Methods 5, 1047–1052 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Shin, J.Y. et al. Visualization and functional dissection of coaxial paired SpoIIIE channels across the sporulation septum. Elife 4 (2015).
• Puchner, E.M., Walter, J.M., Kasper, R., Huang, B. & Lim, W.A. Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory. Proc. Natl. Acad. Sci. USA 110, 16015–16020 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Lee, S.-H., Shin, J.Y., Lee, A. & Bustamante, C. Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM). Proc. Natl. Acad. Sci. USA 109, 17436–17441 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Rollins, G.C., Shin, J.Y., Bustamante, C. & Pressé, S. Stochastic approach to the molecular counting problem in superresolution microscopy. Proc. Natl. Acad. Sci. USA 112, E110–8 (2015).
  Article CAS PubMed Google Scholar
• Nieuwenhuizen, R.P.J. et al. Quantitative localization microscopy: effects of photophysics and labeling stoichiometry. PLoS One 10, e0127989 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Sengupta, P., Jovanovic-Talisman, T. & Lippincott-Schwartz, J. Quantifying spatial organization in point-localization superresolution images using pair correlation analysis. Nat. Protoc. 8, 345–354 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Juette, M.F. et al. Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples. Nat. Methods 5, 527–529 (2008).
  Article CAS PubMed Google Scholar
• Broeken, J. et al. Resolution improvement by 3D particle averaging in localization microscopy. Methods Appl. Fluoresc. 3, 014003 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Cheng, Y., Yifan, C., Nikolaus, G., Penczek, P.A. & Thomas, W. A primer to single-particle cryo-electron microscopy. Cell 161, 438–449 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Szymborska, A. et al. Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging. Science 341, 655–658 (2013).
  Article CAS PubMed Google Scholar
• Loschberger, A. et al. Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution. J. Cell Sci. 125, 570–575 (2012).
  Article PubMed CAS Google Scholar
• Penczek, P., Radermacher, M. & Frank, J. Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 40, 33–53 (1992).
  Article CAS PubMed Google Scholar
• Perrault, S.D. & Chan, W.C.W. Synthesis and surface modification of highly monodispersed, spherical gold nanoparticles of 50-200 nm. J. Am. Chem. Soc. 131, 17042–17043 (2009).
  Article CAS PubMed Google Scholar