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3D DNA Nanostructure pp 185–202Cite as

DNA-PAINT Super-Resolution Imaging for Nucleic Acid Nanostructures

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1500))

Abstract

Far-field super-resolution fluorescence microscopy has allowed observation of biomolecular and synthetic nanoscale systems with features on the nanometre scale, with chemical specificity and multiplexing capability. DNA-PAINT (DNA-based point accumulation for imaging in nanoscale topography) is a super-resolution method that exploits programmable transient hybridization between short oligonucleotide strands, and allows multiplexed, single-molecule, single-label visualization with down to ~5–10 nm resolution. DNA-PAINT provides a method for structural characterisation of nucleic acid nanostructures with high spatial resolution and single-strand visibility.

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Notes

  1. 1.

    Not to be confused with blinking SNR, which is calculated in a single recorded frame.

References

  1. Hell S et al (2015) The 2015 super-resolution microscopy roadmap. J Phys D Appl Phys 48:443001

    Article  Google Scholar 

  2. Huang B, Bates M, Zhuang X (2009) Super-resolution fluorescence microscopy. Annu Rev Biochem 78:993–1016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Sahl SJ, Moerner WE (2013) Super-resolution fluorescence imaging with single molecules. Curr Opin Struct Biol 23:778–787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Betzig E et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645

    Article  CAS  PubMed  Google Scholar 

  5. Hess ST, Girirajan TP, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91:4258–4272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. 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  PubMed Central  Google Scholar 

  7. Heilemann 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 

  8. Sharonov A, Hochstrasser RM (2006) Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proc Natl Acad Sci U S A 103:18911–18916

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Jungmann R et al (2010) Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett 10:4756–4761

    Article  CAS  PubMed  Google Scholar 

  10. Giannone G et al (2010) Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density. Biophys J 99:1303–1310

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Schoen I, Ries J, Klotzsch E, Ewers H, Vogel V (2011) Binding-activated localization microscopy of DNA structures. Nano Lett 11:4008–4011

    Article  CAS  PubMed  Google Scholar 

  12. Johnson-Buck A, Nangreave J, Jiang S, Yan H, Walter NG (2013) Multifactorial modulation of binding and dissociation kinetics on two-dimensional DNA nanostructures. Nano Lett 13:2754–2759

    Article  CAS  PubMed  Google Scholar 

  13. Johnson-Buck A et al (2013) Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Lett 13:728–733

    Article  CAS  PubMed  Google Scholar 

  14. Jungmann R et al (2014) Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and exchange-PAINT. Nat Methods 11:313–318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Jungmann R et al (2016) Quantitative superresolution imaging with qPAINT using transient binding analysis. Nat Methods. doi:10.1038/nmeth.3804

    PubMed Central  Google Scholar 

  16. Dai M, Jungmann R, Yin P (2016) Optical imaging of individual biomolecules in densely packed clusters. Nat. Nanotech. doi:10.1038/nnano.2016.95

  17. Zadeh JN et al (2011) NUPACK: analysis and design of nucleic acid systems. J Comput Chem 32:170–173

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Author information

Authors and Affiliations

  1. Wyss Institute for Biologically Inspired Engineering, Harvard University, CLSB 5th Floor, Blackfan Circle, Boston, MA, 02115, USA

    Mingjie Dai

  2. Program in Biophysics, Harvard University, Boston, MA, 02115, USA

    Mingjie Dai

Authors
  1. Mingjie Dai
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Corresponding author

Correspondence to Mingjie Dai .

Editor information

Editors and Affiliations

  1. Biomolecular Nanoengineering Laboratory, Emory University, Atlanta, Georgia, USA

    Yonggang Ke

  2. Biomolecular Nanoengineering Laboratory, Emory University, Atlanta, Georgia, USA

    Pengfei Wang

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Dai, M. (2017). DNA-PAINT Super-Resolution Imaging for Nucleic Acid Nanostructures. In: Ke, Y., Wang, P. (eds) 3D DNA Nanostructure. Methods in Molecular Biology, vol 1500. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6454-3_13

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  • DOI: https://doi.org/10.1007/978-1-4939-6454-3_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6452-9

  • Online ISBN: 978-1-4939-6454-3

  • eBook Packages: Springer Protocols

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