Abstract

To measure nanometric features with super-resolution requires that the stage, which holds the sample, be stable to nanometric precision. Herein we introduce a new method that uses conventional equipment, is low cost, and does not require intensive computation. Fiduciary markers of approximately 1 µm x 1 µm x 1 µm in x, y, and z dimensions are placed at regular intervals on the coverslip. These fiduciary markers are easy to put down, are completely stationary with respect to the coverslip, are bio-compatible, and do not interfere with fluorescence or intensity measurements. As the coverslip undergoes drift (or is purposely moved), the x-y center of the fiduciary markers can be readily tracked to 1 nanometer using a Gaussian fit. By focusing the light slightly out-of-focus, the z-axis can also be tracked to < 5 nm for dry samples and <17 nm for wet samples by looking at the diffraction rings. The process of tracking the fiduciary markers does not interfere with visible fluorescence because an infrared light emitting diode (IR-LED) (690 and 850 nm) is used, and the IR-light is separately detected using an inexpensive camera. The resulting motion of the coverslip can then be corrected for, either after-the-fact, or by using active stabilizers, to correct for the motion. We applied this method to watch kinesin walking with ≈8 nm steps.

© 2012 OSA

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2011

P. D. Simonson, E. Rothenberg, and P. R. Selvin, “Single-Molecule-Based Super-Resolution Images in the Presence of Multiple Fluorophores,” Nano Lett.11(11), 5090–5096 (2011).
[CrossRef] [PubMed]

D. T. Burnette, P. Sengupta, Y. H. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A.108(52), 21081–21086 (2011).
[CrossRef] [PubMed]

M. J. Mlodzianoski, J. M. Schreiner, S. P. Callahan, K. Smolková, A. Dlasková, J. Santorová, P. Ježek, and J. Bewersdorf, “Sample drift correction in 3D fluorescence photoactivation localization microscopy,” Opt. Express19(16), 15009–15019 (2011).
[CrossRef] [PubMed]

2010

F. Wang, D. Banerjee, Y. S. Liu, X. Y. Chen, and X. G. Liu, “Upconversion nanoparticles in biological labeling, imaging, and therapy,” Analyst (Lond.)135(8), 1839–1854 (2010).
[CrossRef] [PubMed]

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[CrossRef] [PubMed]

D. Qin, Y. N. Xia, and G. M. Whitesides, “Soft lithography for micro- and nanoscale patterning,” Nat. Protoc.5(3), 491–502 (2010).
[CrossRef] [PubMed]

2009

B. Huang, M. Bates, and X. W. Zhuang, “Super-Resolution Fluorescence Microscopy,” Annu. Rev. Biochem.78(1), 993–1016 (2009).
[CrossRef] [PubMed]

E. Toprak, A. Yildiz, M. T. Hoffman, S. S. Rosenfeld, and P. R. Selvin, “Why kinesin is so processive,” Proc. Natl. Acad. Sci. U.S.A.106(31), 12717–12722 (2009).
[CrossRef] [PubMed]

K. M. Zia, M. Zuber, I. A. Bhatti, M. Barikani, and M. A. Sheikh, “Evaluation of biocompatibility and mechanical behavior of polyurethane elastomers based on chitin/1,4-butane diol blends,” Int. J. Biol. Macromol.44(1), 18–22 (2009).
[CrossRef] [PubMed]

2008

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

M. Guizar-Sicairos, S. T. Thurman, and J. R. Fienup, “Efficient subpixel image registration algorithms,” Opt. Lett.33(2), 156–158 (2008).
[CrossRef] [PubMed]

2007

A. R. Carter, G. M. King, T. A. Ulrich, W. Halsey, D. Alchenberger, and T. T. Perkins, “Stabilization of an optical microscope to 0.1 nm in three dimensions,” Appl. Opt.46(3), 421–427 (2007).
[CrossRef] [PubMed]

E. Toprak and P. R. Selvin, “New fluorescent tools for watching nanometer-scale conformational changes of single molecules,” Annu. Rev. Biophys. Biomol. Struct.36(1), 349–369 (2007).
[CrossRef] [PubMed]

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett.7(7), 2043–2045 (2007).
[CrossRef] [PubMed]

S. W. Hell, “Far-field optical nanoscopy,” Science316(5828), 1153–1158 (2007).
[CrossRef] [PubMed]

2006

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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3(10), 793–796 (2006).
[CrossRef] [PubMed]

2005

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A.102(21), 7583–7588 (2005).
[CrossRef] [PubMed]

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A.102(5), 1419–1423 (2005).
[CrossRef] [PubMed]

M. G. L. Gustafsson, “Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution,” Proc. Natl. Acad. Sci. U.S.A.102(37), 13081–13086 (2005).
[CrossRef] [PubMed]

2004

A. Yildiz, M. Tomishige, R. D. Vale, and P. R. Selvin, “Kinesin walks hand-over-hand,” Science303(5658), 676–678 (2004).
[CrossRef] [PubMed]

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A.101(17), 6462–6465 (2004).
[CrossRef] [PubMed]

X. H. Qu, D. Wu, L. Mets, and N. F. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” Proc. Natl. Acad. Sci. U.S.A.101(31), 11298–11303 (2004).
[CrossRef] [PubMed]

L. Nugent-Glandorf and T. T. Perkins, “Measuring 0.1-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection,” Opt. Lett.29(22), 2611–2613 (2004).
[CrossRef] [PubMed]

2003

2002

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise Nanometer Localization Analysis for Individual Fluorescent Probes,” Biophys. J.82(5), 2775–2783 (2002).
[CrossRef] [PubMed]

2000

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

1998

1990

S. M. Block, L. S. B. Goldstein, and B. J. Schnapp, “Bead Movement by Single Kinesin Molecules Studied with Optical Tweezers,” Nature348(6299), 348–352 (1990).
[CrossRef] [PubMed]

1989

Alchenberger, D.

Alivisatos, A. P.

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

Balci, H.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett.7(7), 2043–2045 (2007).
[CrossRef] [PubMed]

Banerjee, D.

F. Wang, D. Banerjee, Y. S. Liu, X. Y. Chen, and X. G. Liu, “Upconversion nanoparticles in biological labeling, imaging, and therapy,” Analyst (Lond.)135(8), 1839–1854 (2010).
[CrossRef] [PubMed]

Barikani, M.

K. M. Zia, M. Zuber, I. A. Bhatti, M. Barikani, and M. A. Sheikh, “Evaluation of biocompatibility and mechanical behavior of polyurethane elastomers based on chitin/1,4-butane diol blends,” Int. J. Biol. Macromol.44(1), 18–22 (2009).
[CrossRef] [PubMed]

Bates, M.

B. Huang, M. Bates, and X. W. Zhuang, “Super-Resolution Fluorescence Microscopy,” Annu. Rev. Biochem.78(1), 993–1016 (2009).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3(10), 793–796 (2006).
[CrossRef] [PubMed]

Bawendi, M. G.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Bewersdorf, J.

Bhatti, I. A.

K. M. Zia, M. Zuber, I. A. Bhatti, M. Barikani, and M. A. Sheikh, “Evaluation of biocompatibility and mechanical behavior of polyurethane elastomers based on chitin/1,4-butane diol blends,” Int. J. Biol. Macromol.44(1), 18–22 (2009).
[CrossRef] [PubMed]

Blehm, B. H.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett.7(7), 2043–2045 (2007).
[CrossRef] [PubMed]

Block, S. M.

S. M. Block, L. S. B. Goldstein, and B. J. Schnapp, “Bead Movement by Single Kinesin Molecules Studied with Optical Tweezers,” Nature348(6299), 348–352 (1990).
[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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Burnette, D. T.

D. T. Burnette, P. Sengupta, Y. H. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A.108(52), 21081–21086 (2011).
[CrossRef] [PubMed]

Callahan, S. P.

Carter, A. R.

Chemla, D. S.

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

Chen, X. Y.

F. Wang, D. Banerjee, Y. S. Liu, X. Y. Chen, and X. G. Liu, “Upconversion nanoparticles in biological labeling, imaging, and therapy,” Analyst (Lond.)135(8), 1839–1854 (2010).
[CrossRef] [PubMed]

Churchman, L. S.

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A.102(5), 1419–1423 (2005).
[CrossRef] [PubMed]

Dai, Y. H.

D. T. Burnette, P. Sengupta, Y. H. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A.108(52), 21081–21086 (2011).
[CrossRef] [PubMed]

Davidson, M. 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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Dawson, J. F.

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A.102(5), 1419–1423 (2005).
[CrossRef] [PubMed]

Dlasková, A.

Fienup, J. R.

Fitzke, F. W.

Florin, E. L.

Fornasiero, E. F.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[CrossRef] [PubMed]

Gibson, S. F.

Girirajan, T. P. K.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

Goldstein, L. S. B.

S. M. Block, L. S. B. Goldstein, and B. J. Schnapp, “Bead Movement by Single Kinesin Molecules Studied with Optical Tweezers,” Nature348(6299), 348–352 (1990).
[CrossRef] [PubMed]

Gordon, M. P.

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A.101(17), 6462–6465 (2004).
[CrossRef] [PubMed]

Guizar-Sicairos, M.

Gustafsson, M. G. L.

M. G. L. Gustafsson, “Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution,” Proc. Natl. Acad. Sci. U.S.A.102(37), 13081–13086 (2005).
[CrossRef] [PubMed]

Ha, T.

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A.101(17), 6462–6465 (2004).
[CrossRef] [PubMed]

Halsey, W.

Hayashi, Y.

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A.102(21), 7583–7588 (2005).
[CrossRef] [PubMed]

Hell, S. W.

S. W. Hell, “Far-field optical nanoscopy,” Science316(5828), 1153–1158 (2007).
[CrossRef] [PubMed]

Henriques, R.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Hess, S. T.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

Hoffman, M. T.

E. Toprak, A. Yildiz, M. T. Hoffman, S. S. Rosenfeld, and P. R. Selvin, “Why kinesin is so processive,” Proc. Natl. Acad. Sci. U.S.A.106(31), 12717–12722 (2009).
[CrossRef] [PubMed]

Howarth, M.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A.102(21), 7583–7588 (2005).
[CrossRef] [PubMed]

Huang, B.

B. Huang, M. Bates, and X. W. Zhuang, “Super-Resolution Fluorescence Microscopy,” Annu. Rev. Biochem.78(1), 993–1016 (2009).
[CrossRef] [PubMed]

Ježek, P.

Jonás, A.

Kachar, B.

D. T. Burnette, P. Sengupta, Y. H. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A.108(52), 21081–21086 (2011).
[CrossRef] [PubMed]

King, G. M.

Lacoste, T. D.

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

Lanni, F.

Larson, D. R.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise Nanometer Localization Analysis for Individual Fluorescent Probes,” Biophys. J.82(5), 2775–2783 (2002).
[CrossRef] [PubMed]

Lelek, M.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Lippincott-Schwartz, J.

D. T. Burnette, P. Sengupta, Y. H. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A.108(52), 21081–21086 (2011).
[CrossRef] [PubMed]

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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Liu, W. H.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

Liu, X. G.

F. Wang, D. Banerjee, Y. S. Liu, X. Y. Chen, and X. G. Liu, “Upconversion nanoparticles in biological labeling, imaging, and therapy,” Analyst (Lond.)135(8), 1839–1854 (2010).
[CrossRef] [PubMed]

Liu, Y. S.

F. Wang, D. Banerjee, Y. S. Liu, X. Y. Chen, and X. G. Liu, “Upconversion nanoparticles in biological labeling, imaging, and therapy,” Analyst (Lond.)135(8), 1839–1854 (2010).
[CrossRef] [PubMed]

Marshall, L. F.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

Mason, M. D.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

Mets, L.

X. H. Qu, D. Wu, L. Mets, and N. F. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” Proc. Natl. Acad. Sci. U.S.A.101(31), 11298–11303 (2004).
[CrossRef] [PubMed]

Mhlanga, M. M.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[CrossRef] [PubMed]

Michalet, X.

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

Mlodzianoski, M. J.

Nugent-Glandorf, L.

Okten, Z.

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A.102(5), 1419–1423 (2005).
[CrossRef] [PubMed]

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,” Science313(5793), 1642–1645 (2006).
[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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Perkins, T. T.

Pinaud, F.

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

Puthenveetil, S.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

Qin, D.

D. Qin, Y. N. Xia, and G. M. Whitesides, “Soft lithography for micro- and nanoscale patterning,” Nat. Protoc.5(3), 491–502 (2010).
[CrossRef] [PubMed]

Qu, X. H.

X. H. Qu, D. Wu, L. Mets, and N. F. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” Proc. Natl. Acad. Sci. U.S.A.101(31), 11298–11303 (2004).
[CrossRef] [PubMed]

Rock, R. S.

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A.102(5), 1419–1423 (2005).
[CrossRef] [PubMed]

Rosenfeld, S. S.

E. Toprak, A. Yildiz, M. T. Hoffman, S. S. Rosenfeld, and P. R. Selvin, “Why kinesin is so processive,” Proc. Natl. Acad. Sci. U.S.A.106(31), 12717–12722 (2009).
[CrossRef] [PubMed]

Rothenberg, E.

P. D. Simonson, E. Rothenberg, and P. R. Selvin, “Single-Molecule-Based Super-Resolution Images in the Presence of Multiple Fluorophores,” Nano Lett.11(11), 5090–5096 (2011).
[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. Methods3(10), 793–796 (2006).
[CrossRef] [PubMed]

Santorová, J.

Scherer, N. F.

X. H. Qu, D. Wu, L. Mets, and N. F. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” Proc. Natl. Acad. Sci. U.S.A.101(31), 11298–11303 (2004).
[CrossRef] [PubMed]

Schmidt, M. M.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

Schnapp, B. J.

S. M. Block, L. S. B. Goldstein, and B. J. Schnapp, “Bead Movement by Single Kinesin Molecules Studied with Optical Tweezers,” Nature348(6299), 348–352 (1990).
[CrossRef] [PubMed]

Schreiner, J. M.

Selvin, P. R.

P. D. Simonson, E. Rothenberg, and P. R. Selvin, “Single-Molecule-Based Super-Resolution Images in the Presence of Multiple Fluorophores,” Nano Lett.11(11), 5090–5096 (2011).
[CrossRef] [PubMed]

E. Toprak, A. Yildiz, M. T. Hoffman, S. S. Rosenfeld, and P. R. Selvin, “Why kinesin is so processive,” Proc. Natl. Acad. Sci. U.S.A.106(31), 12717–12722 (2009).
[CrossRef] [PubMed]

E. Toprak and P. R. Selvin, “New fluorescent tools for watching nanometer-scale conformational changes of single molecules,” Annu. Rev. Biophys. Biomol. Struct.36(1), 349–369 (2007).
[CrossRef] [PubMed]

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett.7(7), 2043–2045 (2007).
[CrossRef] [PubMed]

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A.101(17), 6462–6465 (2004).
[CrossRef] [PubMed]

A. Yildiz, M. Tomishige, R. D. Vale, and P. R. Selvin, “Kinesin walks hand-over-hand,” Science303(5658), 676–678 (2004).
[CrossRef] [PubMed]

Sengupta, P.

D. T. Burnette, P. Sengupta, Y. H. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A.108(52), 21081–21086 (2011).
[CrossRef] [PubMed]

Sheikh, M. A.

K. M. Zia, M. Zuber, I. A. Bhatti, M. Barikani, and M. A. Sheikh, “Evaluation of biocompatibility and mechanical behavior of polyurethane elastomers based on chitin/1,4-butane diol blends,” Int. J. Biol. Macromol.44(1), 18–22 (2009).
[CrossRef] [PubMed]

Simonson, P. D.

P. D. Simonson, E. Rothenberg, and P. R. Selvin, “Single-Molecule-Based Super-Resolution Images in the Presence of Multiple Fluorophores,” Nano Lett.11(11), 5090–5096 (2011).
[CrossRef] [PubMed]

Smolková, K.

Sougrat, R.

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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

Speidel, M.

Spudich, J. A.

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A.102(5), 1419–1423 (2005).
[CrossRef] [PubMed]

Takao, K.

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A.102(21), 7583–7588 (2005).
[CrossRef] [PubMed]

Thompson, R. E.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise Nanometer Localization Analysis for Individual Fluorescent Probes,” Biophys. J.82(5), 2775–2783 (2002).
[CrossRef] [PubMed]

Thurman, S. T.

Ting, A. Y.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A.102(21), 7583–7588 (2005).
[CrossRef] [PubMed]

Tomishige, M.

A. Yildiz, M. Tomishige, R. D. Vale, and P. R. Selvin, “Kinesin walks hand-over-hand,” Science303(5658), 676–678 (2004).
[CrossRef] [PubMed]

Toprak, E.

E. Toprak, A. Yildiz, M. T. Hoffman, S. S. Rosenfeld, and P. R. Selvin, “Why kinesin is so processive,” Proc. Natl. Acad. Sci. U.S.A.106(31), 12717–12722 (2009).
[CrossRef] [PubMed]

E. Toprak and P. R. Selvin, “New fluorescent tools for watching nanometer-scale conformational changes of single molecules,” Annu. Rev. Biophys. Biomol. Struct.36(1), 349–369 (2007).
[CrossRef] [PubMed]

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett.7(7), 2043–2045 (2007).
[CrossRef] [PubMed]

Ulrich, T. A.

Vale, R. D.

A. Yildiz, M. Tomishige, R. D. Vale, and P. R. Selvin, “Kinesin walks hand-over-hand,” Science303(5658), 676–678 (2004).
[CrossRef] [PubMed]

Valtorta, F.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[CrossRef] [PubMed]

Wade, A. R.

Wang, F.

F. Wang, D. Banerjee, Y. S. Liu, X. Y. Chen, and X. G. Liu, “Upconversion nanoparticles in biological labeling, imaging, and therapy,” Analyst (Lond.)135(8), 1839–1854 (2010).
[CrossRef] [PubMed]

Webb, W. W.

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise Nanometer Localization Analysis for Individual Fluorescent Probes,” Biophys. J.82(5), 2775–2783 (2002).
[CrossRef] [PubMed]

Weiss, S.

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

Whitesides, G. M.

D. Qin, Y. N. Xia, and G. M. Whitesides, “Soft lithography for micro- and nanoscale patterning,” Nat. Protoc.5(3), 491–502 (2010).
[CrossRef] [PubMed]

Wittrup, K. D.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

Wu, D.

X. H. Qu, D. Wu, L. Mets, and N. F. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” Proc. Natl. Acad. Sci. U.S.A.101(31), 11298–11303 (2004).
[CrossRef] [PubMed]

Xia, Y. N.

D. Qin, Y. N. Xia, and G. M. Whitesides, “Soft lithography for micro- and nanoscale patterning,” Nat. Protoc.5(3), 491–502 (2010).
[CrossRef] [PubMed]

Yildiz, A.

E. Toprak, A. Yildiz, M. T. Hoffman, S. S. Rosenfeld, and P. R. Selvin, “Why kinesin is so processive,” Proc. Natl. Acad. Sci. U.S.A.106(31), 12717–12722 (2009).
[CrossRef] [PubMed]

A. Yildiz, M. Tomishige, R. D. Vale, and P. R. Selvin, “Kinesin walks hand-over-hand,” Science303(5658), 676–678 (2004).
[CrossRef] [PubMed]

Zheng, Y.

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

Zhuang, X. W.

B. Huang, M. Bates, and X. W. Zhuang, “Super-Resolution Fluorescence Microscopy,” Annu. Rev. Biochem.78(1), 993–1016 (2009).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3(10), 793–796 (2006).
[CrossRef] [PubMed]

Zia, K. M.

K. M. Zia, M. Zuber, I. A. Bhatti, M. Barikani, and M. A. Sheikh, “Evaluation of biocompatibility and mechanical behavior of polyurethane elastomers based on chitin/1,4-butane diol blends,” Int. J. Biol. Macromol.44(1), 18–22 (2009).
[CrossRef] [PubMed]

Zimmer, C.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[CrossRef] [PubMed]

Zuber, M.

K. M. Zia, M. Zuber, I. A. Bhatti, M. Barikani, and M. A. Sheikh, “Evaluation of biocompatibility and mechanical behavior of polyurethane elastomers based on chitin/1,4-butane diol blends,” Int. J. Biol. Macromol.44(1), 18–22 (2009).
[CrossRef] [PubMed]

Analyst (Lond.)

F. Wang, D. Banerjee, Y. S. Liu, X. Y. Chen, and X. G. Liu, “Upconversion nanoparticles in biological labeling, imaging, and therapy,” Analyst (Lond.)135(8), 1839–1854 (2010).
[CrossRef] [PubMed]

Annu. Rev. Biochem.

B. Huang, M. Bates, and X. W. Zhuang, “Super-Resolution Fluorescence Microscopy,” Annu. Rev. Biochem.78(1), 993–1016 (2009).
[CrossRef] [PubMed]

Annu. Rev. Biophys. Biomol. Struct.

E. Toprak and P. R. Selvin, “New fluorescent tools for watching nanometer-scale conformational changes of single molecules,” Annu. Rev. Biophys. Biomol. Struct.36(1), 349–369 (2007).
[CrossRef] [PubMed]

Appl. Opt.

Biophys. J.

S. T. Hess, T. P. K. Girirajan, and M. D. Mason, “Ultra-high resolution imaging by fluorescence photoactivation localization microscopy,” Biophys. J.91(11), 4258–4272 (2006).
[CrossRef] [PubMed]

R. E. Thompson, D. R. Larson, and W. W. Webb, “Precise Nanometer Localization Analysis for Individual Fluorescent Probes,” Biophys. J.82(5), 2775–2783 (2002).
[CrossRef] [PubMed]

Int. J. Biol. Macromol.

K. M. Zia, M. Zuber, I. A. Bhatti, M. Barikani, and M. A. Sheikh, “Evaluation of biocompatibility and mechanical behavior of polyurethane elastomers based on chitin/1,4-butane diol blends,” Int. J. Biol. Macromol.44(1), 18–22 (2009).
[CrossRef] [PubMed]

J. Opt. Soc. Am. A

Nano Lett.

E. Toprak, H. Balci, B. H. Blehm, and P. R. Selvin, “Three-dimensional particle tracking via bifocal imaging,” Nano Lett.7(7), 2043–2045 (2007).
[CrossRef] [PubMed]

P. D. Simonson, E. Rothenberg, and P. R. Selvin, “Single-Molecule-Based Super-Resolution Images in the Presence of Multiple Fluorophores,” Nano Lett.11(11), 5090–5096 (2011).
[CrossRef] [PubMed]

Nat. Methods

M. J. Rust, M. Bates, and X. W. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods3(10), 793–796 (2006).
[CrossRef] [PubMed]

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer, and M. M. Mhlanga, “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ,” Nat. Methods7(5), 339–340 (2010).
[CrossRef] [PubMed]

M. Howarth, W. H. Liu, S. Puthenveetil, Y. Zheng, L. F. Marshall, M. M. Schmidt, K. D. Wittrup, M. G. Bawendi, and A. Y. Ting, “Monovalent, reduced-size quantum dots for imaging receptors on living cells,” Nat. Methods5(5), 397–399 (2008).
[CrossRef] [PubMed]

Nat. Protoc.

D. Qin, Y. N. Xia, and G. M. Whitesides, “Soft lithography for micro- and nanoscale patterning,” Nat. Protoc.5(3), 491–502 (2010).
[CrossRef] [PubMed]

Nature

S. M. Block, L. S. B. Goldstein, and B. J. Schnapp, “Bead Movement by Single Kinesin Molecules Studied with Optical Tweezers,” Nature348(6299), 348–352 (1990).
[CrossRef] [PubMed]

Opt. Express

Opt. Lett.

Proc. Natl. Acad. Sci. U.S.A.

E. Toprak, A. Yildiz, M. T. Hoffman, S. S. Rosenfeld, and P. R. Selvin, “Why kinesin is so processive,” Proc. Natl. Acad. Sci. U.S.A.106(31), 12717–12722 (2009).
[CrossRef] [PubMed]

M. Howarth, K. Takao, Y. Hayashi, and A. Y. Ting, “Targeting quantum dots to surface proteins in living cells with biotin ligase,” Proc. Natl. Acad. Sci. U.S.A.102(21), 7583–7588 (2005).
[CrossRef] [PubMed]

M. G. L. Gustafsson, “Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution,” Proc. Natl. Acad. Sci. U.S.A.102(37), 13081–13086 (2005).
[CrossRef] [PubMed]

M. P. Gordon, T. Ha, and P. R. Selvin, “Single-molecule high-resolution imaging with photobleaching,” Proc. Natl. Acad. Sci. U.S.A.101(17), 6462–6465 (2004).
[CrossRef] [PubMed]

D. T. Burnette, P. Sengupta, Y. H. Dai, J. Lippincott-Schwartz, and B. Kachar, “Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules,” Proc. Natl. Acad. Sci. U.S.A.108(52), 21081–21086 (2011).
[CrossRef] [PubMed]

X. H. Qu, D. Wu, L. Mets, and N. F. Scherer, “Nanometer-localized multiple single-molecule fluorescence microscopy,” Proc. Natl. Acad. Sci. U.S.A.101(31), 11298–11303 (2004).
[CrossRef] [PubMed]

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos, and S. Weiss, “Ultrahigh-resolution multicolor colocalization of single fluorescent probes,” Proc. Natl. Acad. Sci. U.S.A.97(17), 9461–9466 (2000).
[CrossRef] [PubMed]

L. S. Churchman, Z. Okten, R. S. Rock, J. F. Dawson, and J. A. Spudich, “Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time,” Proc. Natl. Acad. Sci. U.S.A.102(5), 1419–1423 (2005).
[CrossRef] [PubMed]

Science

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,” Science313(5793), 1642–1645 (2006).
[CrossRef] [PubMed]

S. W. Hell, “Far-field optical nanoscopy,” Science316(5828), 1153–1158 (2007).
[CrossRef] [PubMed]

A. Yildiz, M. Tomishige, R. D. Vale, and P. R. Selvin, “Kinesin walks hand-over-hand,” Science303(5658), 676–678 (2004).
[CrossRef] [PubMed]

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Figures (5)

Fig. 1
Fig. 1

The optical configuration to track the fiduciary markers using IR scattering with the Total Internal Reflection Fluorescence.

Fig. 2
Fig. 2

(a) IR scattering image for fiduciary markers at different position along the z axis. (Down and up means below and above focal point) Pillars place every 16 μm. (b) Plots for calibration the relation between z-axis distance and ring size of the diffraction pattern.

Fig. 3
Fig. 3

Traces and histograms along x (top), y (middle) and z (bottom) for fiduciary markers. In traces (left panel), green traces are the averaged for traces of four fiduciary markers which are taken for 1 minute. The histograms were taken from the difference between the averaged as compare with each trace. The standard deviations of these histogram are 1.25 nm, 1.47 nm and 16.9 nm for x, y and z, respectively.

Fig. 4
Fig. 4

(a) Traces of kinesin walking. Inset is the zoom in trace. Red line of inset represents the fitting line. (b) traces of the stage drift which is the averaged traces for four fiduciary markers. In case of the uncorrected kinesin trace, it reflects the fluctuation of stage traces. (c) and (d) are histograms for the kinesin step sizes of the corrected and the uncorrected, respectively.

Fig. 5
Fig. 5

Bright field (left) and fluorescence (right) images of the HEK cells cultured on the fiduciary-marked coverslip with quantum dots (605 nm emission; Invitrogen) labeling. In the bright-field image, there are cultured cells as well as regular patterned dots (represented by arrows) which are the fiduciary markers. The fluorescence image has no autofluorescence, showing clear emission spots of the qdots.

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