Abstract

We report detailed characterizations of stochastic fluorescence switching of unmodified nucleic acids under visible light illumination. Although the fluorescent emission from nucleic acids under the visible light illumination has long been overlooked due to their apparent low absorption cross section, our quantitative characterizations reveal the high quantum yield and high photon count in individual fluorescence emission events of nucleic acids at physiological concentrations. Owing to these characteristics, the stochastic fluorescence switching of nucleic acids could be comparable to that of some of the most potent exogenous fluorescence probes for localization-based super-resolution imaging. Therefore, utilizing the principle of single-molecule photon-localization microscopy, native nucleic acids could be ideal candidates for optical label-free super-resolution imaging.

© 2017 Optical Society of America

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    [Crossref] [PubMed]
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    [Crossref]
  23. N. Raghavachari, Y. P. Bao, G. S. Li, X. Y. Xie, and U. R. Muller, “Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride,” Anal. Biochem. 312, 101–105 (2003).
    [Crossref] [PubMed]
  24. S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
    [Crossref] [PubMed]
  25. L. R. Caswell, M. F. Howard, and T. M. Onisto, “Solvent and substituent effects upon n → π* transition of aliphatic carboxylic-acids and esters,” J. Org. Chem. 41, 3312–3316 (1976).
    [Crossref]
  26. I. Buchvarov, Q. Wang, M. Raytchev, A. Trifonov, and T. Fiebig, “Electronic energy delocalization and dissipation in single- and double-stranded DNA,” P. Natl. Acad. Sci. USA 104, 4794–4797 (2007).
    [Crossref]
  27. R. J. Cook and H. J. Kimble, “Possibility of direct observation of quantum jumps,” Phys. Rev. Lett. 54, 1023–1026 (1985).
    [Crossref] [PubMed]
  28. T. Burzykowski, J. Szubiakowski, and T. Ryden, “Analysis of photon count data from single-molecule fluorescence experiments,” Chem. Phys. 288, 291–307 (2003).
    [Crossref]
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  32. F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
    [Crossref] [PubMed]

2016 (5)

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
[Crossref]

B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
[Crossref]

S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
[Crossref] [PubMed]

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

2015 (3)

P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
[Crossref] [PubMed]

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

M. A. Ricci, C. Manzo, M. F. Garcia-Parajo, M. Lakadamyali, and M. P. Cosma, “Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo,” Cell 160, 1145–1158 (2015).
[Crossref] [PubMed]

2012 (1)

A. Bancaud, C. Lavelle, S. Huet, and J. Ellenberg, “A fractal model for nuclear organization: current evidence and biological implications,” Nucleic Acids Res. 40, 8783–8792 (2012).
[Crossref] [PubMed]

2010 (4)

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

I. Vaya, T. Gustavsson, F. A. Miannay, T. Douki, and D. Markovitsi, “Fluorescence of natural DNA: From the femtosecond to the nanosecond time scales,” J. Am. Chem. Soc. 132, 11834–11835 (2010).
[Crossref] [PubMed]

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

2008 (2)

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

T. Takaya, C. Su, K. de La Harpe, C. E. Crespo-Hernandez, and B. Kohler, “UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases,” P. Natl. Acad. Sci. USA 105, 10285–10290 (2008).
[Crossref]

2007 (1)

I. Buchvarov, Q. Wang, M. Raytchev, A. Trifonov, and T. Fiebig, “Electronic energy delocalization and dissipation in single- and double-stranded DNA,” P. Natl. Acad. Sci. USA 104, 4794–4797 (2007).
[Crossref]

2006 (2)

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
[Crossref] [PubMed]

2005 (1)

M. G. L. Gustafsson, “Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution,” P. Natl. Acad. Sci. USA 102, 13081–13086 (2005).
[Crossref]

2003 (4)

R. J. Ellis and A. P. Minton, “Cell biology - Join the crowd,” Nature 425, 27–28 (2003).
[Crossref] [PubMed]

T. Burzykowski, J. Szubiakowski, and T. Ryden, “Analysis of photon count data from single-molecule fluorescence experiments,” Chem. Phys. 288, 291–307 (2003).
[Crossref]

N. Raghavachari, Y. P. Bao, G. S. Li, X. Y. Xie, and U. R. Muller, “Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride,” Anal. Biochem. 312, 101–105 (2003).
[Crossref] [PubMed]

J. R. Daban, “High concentration of DNA in condensed chromatin,” Biochem. Cell Biol. 81, 91–99 (2003).
[Crossref] [PubMed]

2000 (1)

R. Plessow, A. Brockhinke, W. Eimer, and K. Kohse-Hoinghaus, “Intrinsic time- and wavelength-resolved fluorescence of oligonucleotides: A systematic investigation using a novel picosecond laser approach,” J. Phys. Chem. B 104, 3695–3704 (2000).
[Crossref]

1995 (1)

S. W. Hell and M. Kroug, “Ground-State-Depletion Fluorescence Microscopy - A concept for breaking the diffraction resolution limit,” Appl. Phys. B 60, 495–497 (1995).
[Crossref]

1994 (1)

1993 (1)

B. Bohrmann, M. Haider, and E. Kellenberger, “Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM,” Ultramicroscopy 49, 235–251 (1993).
[Crossref] [PubMed]

1992 (1)

T. A. Beerman, M. M. Mchugh, R. Sigmund, J. W. Lown, K. E. Rao, and Y. Bathini, “Effects of Analogs of the DNA minor groove binder Hoechst-33258 on topoisomerase II and I mediated activities,” Biochim. Biophys. Acta 1131, 53–61 (1992).
[Crossref] [PubMed]

1985 (1)

R. J. Cook and H. J. Kimble, “Possibility of direct observation of quantum jumps,” Phys. Rev. Lett. 54, 1023–1026 (1985).
[Crossref] [PubMed]

1981 (1)

A. Anders, “DNA Fluorescence at room-temperature excited by means of a dye-laser,” Chem. Phys. Lett. 81, 270–272 (1981).
[Crossref]

1979 (1)

P. R. Callis, “Polarized fluorescence and estimated lifetimes of the DNA bases at room-temperature,” Chem. Phys. Lett. 61, 563–567 (1979).
[Crossref]

1976 (1)

L. R. Caswell, M. F. Howard, and T. M. Onisto, “Solvent and substituent effects upon n → π* transition of aliphatic carboxylic-acids and esters,” J. Org. Chem. 41, 3312–3316 (1976).
[Crossref]

Agard, D.

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Almassalha, L. M.

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
[Crossref]

B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
[Crossref]

Anders, A.

A. Anders, “DNA Fluorescence at room-temperature excited by means of a dye-laser,” Chem. Phys. Lett. 81, 270–272 (1981).
[Crossref]

Arnold, A. M.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

Backman, V.

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
[Crossref]

B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
[Crossref]

Bancaud, A.

A. Bancaud, C. Lavelle, S. Huet, and J. Ellenberg, “A fractal model for nuclear organization: current evidence and biological implications,” Nucleic Acids Res. 40, 8783–8792 (2012).
[Crossref] [PubMed]

Bao, Y. P.

N. Raghavachari, Y. P. Bao, G. S. Li, X. Y. Xie, and U. R. Muller, “Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride,” Anal. Biochem. 312, 101–105 (2003).
[Crossref] [PubMed]

Bates, M.

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
[Crossref] [PubMed]

Bathini, Y.

T. A. Beerman, M. M. Mchugh, R. Sigmund, J. W. Lown, K. E. Rao, and Y. Bathini, “Effects of Analogs of the DNA minor groove binder Hoechst-33258 on topoisomerase II and I mediated activities,” Biochim. Biophys. Acta 1131, 53–61 (1992).
[Crossref] [PubMed]

Bauer, G. M.

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
[Crossref]

Baumgart, F.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

Beerman, T. A.

T. A. Beerman, M. M. Mchugh, R. Sigmund, J. W. Lown, K. E. Rao, and Y. Bathini, “Effects of Analogs of the DNA minor groove binder Hoechst-33258 on topoisomerase II and I mediated activities,” Biochim. Biophys. Acta 1131, 53–61 (1992).
[Crossref] [PubMed]

Beliveau, B. J.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

Betzig, E.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

Bianco, A.

S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
[Crossref] [PubMed]

Bintu, B.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

Bock, H.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

Boettiger, A. N.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

Bohn, M.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Bohrmann, B.

B. Bohrmann, M. Haider, and E. Kellenberger, “Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM,” Ultramicroscopy 49, 235–251 (1993).
[Crossref] [PubMed]

Bonifacino, J. S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

Bossi, M.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

Boulanger, J.

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Brigante, M.

S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
[Crossref] [PubMed]

Brockhinke, A.

R. Plessow, A. Brockhinke, W. Eimer, and K. Kohse-Hoinghaus, “Intrinsic time- and wavelength-resolved fluorescence of oligonucleotides: A systematic investigation using a novel picosecond laser approach,” J. Phys. Chem. B 104, 3695–3704 (2000).
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Buchvarov, I.

I. Buchvarov, Q. Wang, M. Raytchev, A. Trifonov, and T. Fiebig, “Electronic energy delocalization and dissipation in single- and double-stranded DNA,” P. Natl. Acad. Sci. USA 104, 4794–4797 (2007).
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P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
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A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Caswell, L. R.

L. R. Caswell, M. F. Howard, and T. M. Onisto, “Solvent and substituent effects upon n → π* transition of aliphatic carboxylic-acids and esters,” J. Org. Chem. 41, 3312–3316 (1976).
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Chandel, N.

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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Chandler, J.

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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Chandler, J. E.

B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
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L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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Churchman, L. S.

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Cook, R. J.

R. J. Cook and H. J. Kimble, “Possibility of direct observation of quantum jumps,” Phys. Rev. Lett. 54, 1023–1026 (1985).
[Crossref] [PubMed]

Cope, A. P.

P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
[Crossref] [PubMed]

Cosma, M. P.

M. A. Ricci, C. Manzo, M. F. Garcia-Parajo, M. Lakadamyali, and M. P. Cosma, “Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo,” Cell 160, 1145–1158 (2015).
[Crossref] [PubMed]

Cremer, C.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Crespo-Hernandez, C. E.

T. Takaya, C. Su, K. de La Harpe, C. E. Crespo-Hernandez, and B. Kohler, “UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases,” P. Natl. Acad. Sci. USA 105, 10285–10290 (2008).
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J. R. Daban, “High concentration of DNA in condensed chromatin,” Biochem. Cell Biol. 81, 91–99 (2003).
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E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
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de La Harpe, K.

T. Takaya, C. Su, K. de La Harpe, C. E. Crespo-Hernandez, and B. Kohler, “UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases,” P. Natl. Acad. Sci. USA 105, 10285–10290 (2008).
[Crossref]

Diesinger, P.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Donaldson, D. J.

S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
[Crossref] [PubMed]

Dong, B.

B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
[Crossref]

Douki, T.

I. Vaya, T. Gustavsson, F. A. Miannay, T. Douki, and D. Markovitsi, “Fluorescence of natural DNA: From the femtosecond to the nanosecond time scales,” J. Am. Chem. Soc. 132, 11834–11835 (2010).
[Crossref] [PubMed]

Eggeling, C.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

Eimer, W.

R. Plessow, A. Brockhinke, W. Eimer, and K. Kohse-Hoinghaus, “Intrinsic time- and wavelength-resolved fluorescence of oligonucleotides: A systematic investigation using a novel picosecond laser approach,” J. Phys. Chem. B 104, 3695–3704 (2000).
[Crossref]

Ellenberg, J.

A. Bancaud, C. Lavelle, S. Huet, and J. Ellenberg, “A fractal model for nuclear organization: current evidence and biological implications,” Nucleic Acids Res. 40, 8783–8792 (2012).
[Crossref] [PubMed]

Ellis, R. J.

R. J. Ellis and A. P. Minton, “Cell biology - Join the crowd,” Nature 425, 27–28 (2003).
[Crossref] [PubMed]

Fiebig, T.

I. Buchvarov, Q. Wang, M. Raytchev, A. Trifonov, and T. Fiebig, “Electronic energy delocalization and dissipation in single- and double-stranded DNA,” P. Natl. Acad. Sci. USA 104, 4794–4797 (2007).
[Crossref]

Flyvbjerg, H.

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Folling, J.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

Folser, M.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

Fudenberg, G.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

Garcia-Parajo, M. F.

M. A. Ricci, C. Manzo, M. F. Garcia-Parajo, M. Lakadamyali, and M. P. Cosma, “Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo,” Cell 160, 1145–1158 (2015).
[Crossref] [PubMed]

George, C.

S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
[Crossref] [PubMed]

Gladstein, S.

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
[Crossref]

Griffie, J.

P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
[Crossref] [PubMed]

Gunkel, M.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Gustafsson, M. G. L.

M. G. L. Gustafsson, “Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution,” P. Natl. Acad. Sci. USA 102, 13081–13086 (2005).
[Crossref]

Gustavsson, T.

I. Vaya, T. Gustavsson, F. A. Miannay, T. Douki, and D. Markovitsi, “Fluorescence of natural DNA: From the femtosecond to the nanosecond time scales,” J. Am. Chem. Soc. 132, 11834–11835 (2010).
[Crossref] [PubMed]

Haider, M.

B. Bohrmann, M. Haider, and E. Kellenberger, “Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM,” Ultramicroscopy 49, 235–251 (1993).
[Crossref] [PubMed]

Hausmann, M.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Heard, N. A.

P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
[Crossref] [PubMed]

Heermann, D. W.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Hein, B.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

Hell, S. W.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

S. W. Hell and M. Kroug, “Ground-State-Depletion Fluorescence Microscopy - A concept for breaking the diffraction resolution limit,” Appl. Phys. B 60, 495–497 (1995).
[Crossref]

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

Hess, H. F.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

Howard, M. F.

L. R. Caswell, M. F. Howard, and T. M. Onisto, “Solvent and substituent effects upon n → π* transition of aliphatic carboxylic-acids and esters,” J. Org. Chem. 41, 3312–3316 (1976).
[Crossref]

Huet, S.

A. Bancaud, C. Lavelle, S. Huet, and J. Ellenberg, “A fractal model for nuclear organization: current evidence and biological implications,” Nucleic Acids Res. 40, 8783–8792 (2012).
[Crossref] [PubMed]

Imakaev, M.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

Jakobs, S.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

Kaufmann, R.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Kellenberger, E.

B. Bohrmann, M. Haider, and E. Kellenberger, “Concentration evaluation of chromatin in unstained resin-embedded sections by means of low-dose ratio-contrast imaging in STEM,” Ultramicroscopy 49, 235–251 (1993).
[Crossref] [PubMed]

Kervrann, C.

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Kimble, H. J.

R. J. Cook and H. J. Kimble, “Possibility of direct observation of quantum jumps,” Phys. Rev. Lett. 54, 1023–1026 (1985).
[Crossref] [PubMed]

Kirshner, H.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Kner, P.

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Kohler, B.

T. Takaya, C. Su, K. de La Harpe, C. E. Crespo-Hernandez, and B. Kohler, “UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases,” P. Natl. Acad. Sci. USA 105, 10285–10290 (2008).
[Crossref]

Kohse-Hoinghaus, K.

R. Plessow, A. Brockhinke, W. Eimer, and K. Kohse-Hoinghaus, “Intrinsic time- and wavelength-resolved fluorescence of oligonucleotides: A systematic investigation using a novel picosecond laser approach,” J. Phys. Chem. B 104, 3695–3704 (2000).
[Crossref]

Kroug, M.

S. W. Hell and M. Kroug, “Ground-State-Depletion Fluorescence Microscopy - A concept for breaking the diffraction resolution limit,” Appl. Phys. B 60, 495–497 (1995).
[Crossref]

Lakadamyali, M.

M. A. Ricci, C. Manzo, M. F. Garcia-Parajo, M. Lakadamyali, and M. P. Cosma, “Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo,” Cell 160, 1145–1158 (2015).
[Crossref] [PubMed]

Lavelle, C.

A. Bancaud, C. Lavelle, S. Huet, and J. Ellenberg, “A fractal model for nuclear organization: current evidence and biological implications,” Nucleic Acids Res. 40, 8783–8792 (2012).
[Crossref] [PubMed]

Lemmer, P.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Leskovar, K.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

Li, G. S.

N. Raghavachari, Y. P. Bao, G. S. Li, X. Y. Xie, and U. R. Muller, “Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride,” Anal. Biochem. 312, 101–105 (2003).
[Crossref] [PubMed]

Lindwasser, O. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

Lippincott-Schwartz, J.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

Lown, J. W.

T. A. Beerman, M. M. Mchugh, R. Sigmund, J. W. Lown, K. E. Rao, and Y. Bathini, “Effects of Analogs of the DNA minor groove binder Hoechst-33258 on topoisomerase II and I mediated activities,” Biochim. Biophys. Acta 1131, 53–61 (1992).
[Crossref] [PubMed]

Manley, S.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Manzo, C.

M. A. Ricci, C. Manzo, M. F. Garcia-Parajo, M. Lakadamyali, and M. P. Cosma, “Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo,” Cell 160, 1145–1158 (2015).
[Crossref] [PubMed]

Markovitsi, D.

I. Vaya, T. Gustavsson, F. A. Miannay, T. Douki, and D. Markovitsi, “Fluorescence of natural DNA: From the femtosecond to the nanosecond time scales,” J. Am. Chem. Soc. 132, 11834–11835 (2010).
[Crossref] [PubMed]

Matsuda, A.

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Mchugh, M. M.

T. A. Beerman, M. M. Mchugh, R. Sigmund, J. W. Lown, K. E. Rao, and Y. Bathini, “Effects of Analogs of the DNA minor groove binder Hoechst-33258 on topoisomerase II and I mediated activities,” Biochim. Biophys. Acta 1131, 53–61 (1992).
[Crossref] [PubMed]

Medda, R.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
[Crossref] [PubMed]

Miannay, F. A.

I. Vaya, T. Gustavsson, F. A. Miannay, T. Douki, and D. Markovitsi, “Fluorescence of natural DNA: From the femtosecond to the nanosecond time scales,” J. Am. Chem. Soc. 132, 11834–11835 (2010).
[Crossref] [PubMed]

Min, J.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Minton, A. P.

R. J. Ellis and A. P. Minton, “Cell biology - Join the crowd,” Nature 425, 27–28 (2003).
[Crossref] [PubMed]

Mirny, L. A.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

Moffitt, J. R.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
[Crossref] [PubMed]

Mortensen, K. I.

K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

Muller, P.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
[Crossref] [PubMed]

Muller, U. R.

N. Raghavachari, Y. P. Bao, G. S. Li, X. Y. Xie, and U. R. Muller, “Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride,” Anal. Biochem. 312, 101–105 (2003).
[Crossref] [PubMed]

Nguyen, T. Q.

B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
[Crossref]

Olenych, S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

Onisto, T. M.

L. R. Caswell, M. F. Howard, and T. M. Onisto, “Solvent and substituent effects upon n → π* transition of aliphatic carboxylic-acids and esters,” J. Org. Chem. 41, 3312–3316 (1976).
[Crossref]

Owen, D. M.

P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
[Crossref] [PubMed]

Passananti, M.

S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
[Crossref] [PubMed]

Patterson, G. H.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

Pengo, T.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Plessow, R.

R. Plessow, A. Brockhinke, W. Eimer, and K. Kohse-Hoinghaus, “Intrinsic time- and wavelength-resolved fluorescence of oligonucleotides: A systematic investigation using a novel picosecond laser approach,” J. Phys. Chem. B 104, 3695–3704 (2000).
[Crossref]

Raghavachari, N.

N. Raghavachari, Y. P. Bao, G. S. Li, X. Y. Xie, and U. R. Muller, “Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride,” Anal. Biochem. 312, 101–105 (2003).
[Crossref] [PubMed]

Rao, K. E.

T. A. Beerman, M. M. Mchugh, R. Sigmund, J. W. Lown, K. E. Rao, and Y. Bathini, “Effects of Analogs of the DNA minor groove binder Hoechst-33258 on topoisomerase II and I mediated activities,” Biochim. Biophys. Acta 1131, 53–61 (1992).
[Crossref] [PubMed]

Raytchev, M.

I. Buchvarov, Q. Wang, M. Raytchev, A. Trifonov, and T. Fiebig, “Electronic energy delocalization and dissipation in single- and double-stranded DNA,” P. Natl. Acad. Sci. USA 104, 4794–4797 (2007).
[Crossref]

Ricci, M. A.

M. A. Ricci, C. Manzo, M. F. Garcia-Parajo, M. Lakadamyali, and M. P. Cosma, “Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo,” Cell 160, 1145–1158 (2015).
[Crossref] [PubMed]

Rossignol, S.

S. Rossignol, L. Tinel, A. Bianco, M. Passananti, M. Brigante, D. J. Donaldson, and C. George, “Atmospheric photochemistry at a fatty acid–coated air-water interface,” Science 353, 699–702 (2016).
[Crossref] [PubMed]

Roy, H.

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
[Crossref]

Rubin-Delanchy, P.

P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
[Crossref] [PubMed]

Rust, M. J.

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
[Crossref] [PubMed]

Ryden, T.

T. Burzykowski, J. Szubiakowski, and T. Ryden, “Analysis of photon count data from single-molecule fluorescence experiments,” Chem. Phys. 288, 291–307 (2003).
[Crossref]

Sage, D.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
[Crossref] [PubMed]

Schutz, G. J.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

Sedat, J. W.

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Shao, L.

A. Matsuda, L. Shao, J. Boulanger, C. Kervrann, P. M. Carlton, P. Kner, D. Agard, and J. W. Sedat, “Condensed mitotic chromosome structure at nanometer resolution using PALM and EGFP-histones,” Plos One 5, e12768 (2010).
[Crossref]

Sigmund, R.

T. A. Beerman, M. M. Mchugh, R. Sigmund, J. W. Lown, K. E. Rao, and Y. Bathini, “Effects of Analogs of the DNA minor groove binder Hoechst-33258 on topoisomerase II and I mediated activities,” Biochim. Biophys. Acta 1131, 53–61 (1992).
[Crossref] [PubMed]

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E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645 (2006).
[Crossref] [PubMed]

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K. I. Mortensen, L. S. Churchman, J. A. Spudich, and H. Flyvbjerg, “Optimized localization analysis for single-molecule tracking and super-resolution microscopy,” Nat. Methods 7, 377–381 (2010).
[Crossref] [PubMed]

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F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

Stockinger, H.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
[Crossref] [PubMed]

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D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
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B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
[Crossref]

L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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T. Takaya, C. Su, K. de La Harpe, C. E. Crespo-Hernandez, and B. Kohler, “UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases,” P. Natl. Acad. Sci. USA 105, 10285–10290 (2008).
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L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
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L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
[Crossref]

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T. Burzykowski, J. Szubiakowski, and T. Ryden, “Analysis of photon count data from single-molecule fluorescence experiments,” Chem. Phys. 288, 291–307 (2003).
[Crossref]

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T. Takaya, C. Su, K. de La Harpe, C. E. Crespo-Hernandez, and B. Kohler, “UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases,” P. Natl. Acad. Sci. USA 105, 10285–10290 (2008).
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L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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I. Buchvarov, Q. Wang, M. Raytchev, A. Trifonov, and T. Fiebig, “Electronic energy delocalization and dissipation in single- and double-stranded DNA,” P. Natl. Acad. Sci. USA 104, 4794–4797 (2007).
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D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, “Quantitative evaluation of software packages for single-molecule localization microscopy,” Nat. Methods 12, 717–724 (2015).
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B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
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I. Buchvarov, Q. Wang, M. Raytchev, A. Trifonov, and T. Fiebig, “Electronic energy delocalization and dissipation in single- and double-stranded DNA,” P. Natl. Acad. Sci. USA 104, 4794–4797 (2007).
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F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Folser, J. Weghuber, H. Stockinger, and G. J. Schutz, “Varying label density allows artifact-free analysis of membrane-protein nanoclusters,” Nat. Methods 13, 661–664 (2016).
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M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Muller, M. Gunkel, A. von Ketteler, P. Lemmer, M. Hausmann, D. W. Heermann, and C. Cremer, “Localization microscopy reveals expression-dependent parameters of chromatin nanostructure,” Biophys. J. 99, 1358–1367 (2010).
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L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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P. Rubin-Delanchy, G. L. Burn, J. Griffie, D. J. Williamson, N. A. Heard, A. P. Cope, and D. M. Owen, “Bayesian cluster identification in single-molecule localization microscopy data,” Nat. Methods 12, 1072–1076 (2015).
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A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau, G. Fudenberg, M. Imakaev, L. A. Mirny, C. T. Wu, and X. Zhuang, “Super-resolution imaging reveals distinct chromatin folding for different epigenetic states,” Nature 529, 418–422 (2016).
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J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm, B. Hein, S. Jakobs, C. Eggeling, and S. W. Hell, “Fluorescence nanoscopy by ground-state depletion and single-molecule return,” Nat. Methods 5, 943–945 (2008).
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L. M. Almassalha, G. M. Bauer, J. Chandler, S. Gladstein, L. Cherkezyan, Y. Stypula-Cyrus, S. Weinberg, D. Zhang, P. Thusgaard Ruhoff, H. Roy, H. Subramanian, N. Chandel, I. Szleifer, and V. Backman, “Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy,” P. Natl. Acad. Sci. USA 113E6372–E6381 (2016).
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B. Dong, L. M. Almassalha, Y. Stypula-Cyrus, B. E. Urban, J. E. Chandler, T. Q. Nguyen, C. Sun, H. F. Zhang, and V. Backman, “Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast,” P. Natl. Acad. Sci. USA 113, 9716–9721 (2016).
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M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–795 (2006).
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Figures (10)

Fig. 1
Fig. 1 Schematic of the experimental setup for single-molecule photon localization microscopy. LF: laser clean-up filter; SF: spatial filter; HWP: achromatic half-wave plate; GTP: Glan-Taylor polarizer; DM: dichroic mirror; OBJ: objective lens; LPF: long-pass filter; RM: reflecting mirror; TL: tube lens; EMCCD: electron multiplying charge coupled device.
Fig. 2
Fig. 2 Max projection images and number of blinking events over 50 seconds under various conditions: (a) coverslip surface treated by plasma cleanering; (b) water-coated coverslip; and (c) polynucleotides deposited coverslip. The results show at least 99% of the blinking is from polynucleotides.
Fig. 3
Fig. 3 (a) Absorbance spectra of guanine monophosphate as a function of concentration. (b) Absorbance spectra of 0.1-M mononucleotide solutions.
Fig. 4
Fig. 4 Normalized HPLC DAD absorption spectra of 20-base polynucleotide synthesized by IDT. Impurity is observed at 65 minutes as measured by 230 nm absorbance and is demarked by the arrow. Under 532 nm, this band does not show detectable absorbance above the baseline measurements performed on HPLC grade water (H2O) at the same time. Additionally, the purified elusion band consisting of pure polynucleotide demonstrates significant measureable absorbance at 532 nm.
Fig. 5
Fig. 5 Molar extinction coefficient of 20-base poly-G nucleotide was measured using its aqueous solution with concentration of 100-μM. Measurement was performed in a 45-μL cuvette with a path length of 3-mm using a UV-VIS Spectrophotometer (UV-1800, Shimadzu). The Molar extinction coefficient of mononucleotide was measured under same condition for comparison.
Fig. 6
Fig. 6 (a) Fluorescence intensity per nucleotide with respect to oligomer lengths. Fluorescence of polynucleotides with 1-, 2-, 4-, 8-, 16- and 20-base were excited at 500 nm. Comparison of (b) fluorescence intensity per nucleotide and (c) Molar extinction coefficient per nucleotide for mononucleotide and 20-base polynucleotide. Critically, this indicates a non-linear relation between sequence length, fluorescence intensity, and excitation coefficient.
Fig. 7
Fig. 7 Population of the ground state ε of four types of polynucleotides as function of Iex and their linear regression (solid lines). Inset: Jablonski diagram of a three level system.
Fig. 8
Fig. 8 Fluorescence recovery of poly-G DNA after 100 ms dark state shelving with Ipump up to 24 kWcm−2. The recovered signal (black line) was read out with Iprobe (532 nm, 0.3 kWcm−2), which can be accurately explained by the GSD model (red line). The recovery time τ and Φ were obtained by fitting the GSD model to the data.
Fig. 9
Fig. 9 (a) Consecutive images acquired from poly-G DNA sample with time interval of 10 ms, showing blinking events. (b) The illustration shows a typical fluorescence switching process. (c) Fluorescent photon count NB versus blinking duration τB at Iex=7.14 kWcm−2. Color was used to denote the density of data spots. Histograms of (d) τB and (e) NB follow exponential distribution.
Fig. 10
Fig. 10 (a) Fluorescent photon emission rate Γ during “on” times, (b) mean blinking time τB and (c) mean photon count NB as a function of Iex, respectively. In steady state the model accurately explained the Γ, τB and NB as a function of Iex.

Tables (1)

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Table 1 Comparison of recovery lifetime and averaged photon count and blinking time at Iex=7.14 kWcm−2 between four polynuceotides.

Equations (8)

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{ d n 0 d t = k ex n 0 + k fl n 1 + k n 2 d n 1 d t = + k ex n 0 k fl n 1 k isc n 1 , d n 2 d t = + k isc n 1 k n 2
n 0 = 1 1 + k ex ( k + k isc ) k ( k fl + k isc )
n 0 = 1 1 + k + k isc k k isc Φ k ex 1 1 + Φ k ex k = 1 1 + Φ τ k ex
ε = F / F 0 1 / ( 1 + Φ τ k ex ) ,
n 0 = { 1 + k pump Φ e k ( 1 + k pump Φ ) t τ 1 + k pump Φ , if t t d 1 + k pump Φ e k ( 1 + k pump Φ ) t d τ 1 + k pump Φ e k ( 1 + k probe Φ ) t t d τ 1 + 1 + k pump Φ e k ( 1 + k probe Φ ) t t d τ 1 + k probe Φ , if t > t d
Γ = Q Y I ex σ h ν .
1 τ B = Φ I ex σ h ν .
N B = Γ τ B = Q Y Φ .

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