Abstract

Resolving single fluorescent molecules in the presence of high fluorophore concentrations remains a challenge in single-molecule biophysics that limits our understanding of weak molecular interactions. Total internal reflection fluorescence (TIRF) imaging, the workhorse of single-molecule fluorescence microscopy, enables experiments at concentrations up to about 100 nM, but many biological interactions have considerably weaker affinities, and thus require at least one species to be at micromolar or higher concentration. Current alternatives to TIRF often require three-dimensional confinement, and thus can be problematic for extended substrates, such as cytoskeletal filaments. To address this challenge, we have demonstrated and applied two new single-molecule fluorescence microscopy techniques, linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC), for imaging the processive motion of molecular motors myosin V and VI along actin filaments. Both technologies will allow imaging in the presence of higher fluorophore concentrations than TIRF microscopy. They will enable new biophysical measurements of a wide range of processive molecular motors that move along filamentous tracks, such as other myosins, dynein, and kinesin. A particularly salient application of these technologies will be to examine chemomechanical coupling by directly imaging fluorescent nucleotide molecules interacting with processive motors as they traverse their actin or microtubule tracks.

© 2013 OSA

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2012 (3)

A. B. Loveland, S. Habuchi, J. C. Walter, and A. M. van Oijen, “A general approach to break the concentration barrier in single-molecule imaging,” Nat. Methods 9(10), 987–992 (2012).
[Crossref] [PubMed]

W. Qiu, N. D. Derr, B. S. Goodman, E. Villa, D. Wu, W. Shih, and S. L. Reck-Peterson, “Dynein achieves processive motion using both stochastic and coordinated stepping,” Nat. Struct. Mol. Biol. 19(2), 193–200 (2012).
[Crossref] [PubMed]

M. A. DeWitt, A. Y. Chang, P. A. Combs, and A. Yildiz, “Cytoplasmic dynein moves through uncoordinated stepping of the AAA+ ring domains,” Science 335(6065), 221–225 (2012).
[Crossref] [PubMed]

2011 (1)

M. W. Elting, Z. Bryant, J. C. Liao, and J. A. Spudich, “Detailed tuning of structure and intramolecular communication are dispensable for processive motion of myosin VI,” Biophys. J. 100(2), 430–439 (2011).
[Crossref] [PubMed]

2010 (4)

A. R. Dunn, P. Chuan, Z. Bryant, and J. A. Spudich, “Contribution of the myosin VI tail domain to processive stepping and intramolecular tension sensing,” Proc. Natl. Acad. Sci. U.S.A. 107(17), 7746–7750 (2010).
[Crossref] [PubMed]

S. Uemura, C. E. Aitken, J. Korlach, B. A. Flusberg, S. W. Turner, and J. D. Puglisi, “Real-time tRNA transit on single translating ribosomes at codon resolution,” Nature 464(7291), 1012–1017 (2010).
[Crossref] [PubMed]

S. R. Leslie, A. P. Fields, and A. E. Cohen, “Convex lens-induced confinement for imaging single molecules,” Anal. Chem. 82(14), 6224–6229 (2010).
[Crossref] [PubMed]

J. J. Benítez, A. M. Keller, and P. Chen, “Nanovesicle trapping for studying weak protein interactions by single-molecule FRET,” Methods Enzymol. 472, 41–60 (2010).
[Crossref] [PubMed]

2009 (5)

B. Okumus, S. Arslan, S. M. Fengler, S. Myong, and T. Ha, “Single molecule nanocontainers made porous using a bacterial toxin,” J. Am. Chem. Soc. 131(41), 14844–14849 (2009).
[Crossref] [PubMed]

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, and T. Yanagida, “Simultaneous measurement of nucleotide occupancy and mechanical displacement in myosin-V, a processive molecular motor,” Biophys. J. 96(1), L04–L06 (2009).
[Crossref] [PubMed]

D. T. Chiu, R. M. Lorenz, and G. D. M. Jeffries, “Droplets for ultrasmall-volume analysis,” Anal. Chem. 81(13), 5111–5118 (2009).
[Crossref] [PubMed]

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

J.-C. Liao, M. W. Elting, S. L. Delp, J. A. Spudich, and Z. Bryant, “Engineered myosin VI motors reveal minimal structural determinants of directionality and processivity,” J. Mol. Biol. 392(4), 862–867 (2009).
[Crossref] [PubMed]

2008 (4)

J. Korlach, P. J. Marks, R. L. Cicero, J. J. Gray, D. L. Murphy, D. B. Roitman, T. T. Pham, G. A. Otto, M. Foquet, and S. W. Turner, “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures,” Proc. Natl. Acad. Sci. U.S.A. 105(4), 1176–1181 (2008).
[Crossref] [PubMed]

Y. Oguchi, S. V. Mikhailenko, T. Ohki, A. O. Olivares, E. M. De La Cruz, and S. Ishiwata, “Load-dependent ADP binding to myosins V and VI: implications for subunit coordination and function,” Proc. Natl. Acad. Sci. U.S.A. 105(22), 7714–7719 (2008).
[Crossref] [PubMed]

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, and T. Yanagida, “Measurement system for simultaneous observation of myosin V chemical and mechanical events,” Biosystems 93(1-2), 48–57 (2008).
[Crossref] [PubMed]

T. Sakamoto, M. R. Webb, E. Forgacs, H. D. White, and J. R. Sellers, “Direct observation of the mechanochemical coupling in myosin Va during processive movement,” Nature 455(7209), 128–132 (2008).
[Crossref] [PubMed]

2007 (3)

S. M. Block, “Kinesin motor mechanics: binding, stepping, tracking, gating, and limping,” Biophys. J. 92(9), 2986–2995 (2007).
[Crossref] [PubMed]

K. Adachi, K. Oiwa, T. Nishizaka, S. Furuike, H. Noji, H. Itoh, M. Yoshida, and K. Kinosita., “Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation,” Cell 130(2), 309–321 (2007).
[Crossref] [PubMed]

H. L. Sweeney, H. Park, A. B. Zong, Z. Yang, P. R. Selvin, and S. S. Rosenfeld, “How myosin VI coordinates its heads during processive movement,” EMBO J. 26(11), 2682–2692 (2007).
[Crossref] [PubMed]

2006 (1)

R. Carballido-López, “The bacterial actin-like cytoskeleton,” Microbiol. Mol. Biol. Rev. 70(4), 888–909 (2006).
[Crossref] [PubMed]

2005 (2)

J. Wenger, P.-F. Lenne, E. Popov, H. Rigneault, J. Dintinger, and T. Ebbesen, “Single molecule fluorescence in rectangular nano-apertures,” Opt. Express 13(18), 7035–7044 (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]

2003 (1)

M. J. Levene, J. Korlach, S. W. Turner, M. Foquet, H. G. Craighead, and W. W. Webb, “Zero-mode waveguides for single-molecule analysis at high concentrations,” Science 299(5607), 682–686 (2003).
[Crossref] [PubMed]

2002 (2)

R. Littlefield and V. M. Fowler, “A minor actin catastrophe,” Nat. Cell Biol. 4(9), E209–E211 (2002).
[Crossref] [PubMed]

I. Fujiwara, S. Takahashi, H. Tadakuma, T. Funatsu, and S. Ishiwata, “Microscopic analysis of polymerization dynamics with individual actin filaments,” Nat. Cell Biol. 4(9), 666–673 (2002).
[Crossref] [PubMed]

2001 (2)

E. Boukobza, A. Sonnenfeld, and G. Haran, “Immobilization in Surface-Tethered Lipid Vesicles as a New Tool for Single Biomolecule Spectroscopy,” J. Phys. Chem. B 105(48), 12165–12170 (2001).
[Crossref]

E. M. De La Cruz, E. M. Ostap, and H. L. Sweeney, “Kinetic mechanism and regulation of myosin VI,” J. Biol. Chem. 276(34), 32373–32381 (2001).
[Crossref] [PubMed]

2000 (2)

M. Rief, R. S. Rock, A. D. Mehta, M. S. Mooseker, R. E. Cheney, and J. A. Spudich, “Myosin-V stepping kinetics: a molecular model for processivity,” Proc. Natl. Acad. Sci. U.S.A. 97(17), 9482–9486 (2000).
[Crossref] [PubMed]

K. Oiwa, J. F. Eccleston, M. Anson, M. Kikumoto, C. T. Davis, G. P. Reid, M. A. Ferenczi, J. E. Corrie, A. Yamada, H. Nakayama, and D. R. Trentham, “Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives,” Biophys. J. 78(6), 3048–3071 (2000).
[Crossref] [PubMed]

1998 (1)

A. Ishijima, H. Kojima, T. Funatsu, M. Tokunaga, H. Higuchi, H. Tanaka, and T. Yanagida, “Simultaneous observation of individual ATPase and mechanical events by a single myosin molecule during interaction with actin,” Cell 92(2), 161–171 (1998).
[Crossref] [PubMed]

1997 (2)

M. Tokunaga, K. Kitamura, K. Saito, A. H. Iwane, and T. Yanagida, “Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy,” Biochem. Biophys. Res. Commun. 235(1), 47–53 (1997).
[Crossref] [PubMed]

T. Funatsu, Y. Harada, H. Higuchi, M. Tokunaga, K. Saito, Y. Ishii, R. D. Vale, and T. Yanagida, “Imaging and nano-manipulation of single biomolecules,” Biophys. Chem. 68(1-3), 63–72 (1997).
[Crossref] [PubMed]

1992 (1)

J. A. Theriot and T. J. Mitchison, “The nucleation-release model of actin filament dynamics in cell motility,” Trends Cell Biol. 2(8), 219–222 (1992).
[Crossref] [PubMed]

1982 (1)

J. D. Pardee and J. A. Spudich, “Purification of muscle actin,” Methods Cell Biol. 24, 271–289 (1982).
[Crossref] [PubMed]

Adachi, K.

K. Adachi, K. Oiwa, T. Nishizaka, S. Furuike, H. Noji, H. Itoh, M. Yoshida, and K. Kinosita., “Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation,” Cell 130(2), 309–321 (2007).
[Crossref] [PubMed]

Aitken, C. E.

S. Uemura, C. E. Aitken, J. Korlach, B. A. Flusberg, S. W. Turner, and J. D. Puglisi, “Real-time tRNA transit on single translating ribosomes at codon resolution,” Nature 464(7291), 1012–1017 (2010).
[Crossref] [PubMed]

Anson, M.

K. Oiwa, J. F. Eccleston, M. Anson, M. Kikumoto, C. T. Davis, G. P. Reid, M. A. Ferenczi, J. E. Corrie, A. Yamada, H. Nakayama, and D. R. Trentham, “Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives,” Biophys. J. 78(6), 3048–3071 (2000).
[Crossref] [PubMed]

Ariga, T.

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, and T. Yanagida, “Simultaneous measurement of nucleotide occupancy and mechanical displacement in myosin-V, a processive molecular motor,” Biophys. J. 96(1), L04–L06 (2009).
[Crossref] [PubMed]

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, and T. Yanagida, “Measurement system for simultaneous observation of myosin V chemical and mechanical events,” Biosystems 93(1-2), 48–57 (2008).
[Crossref] [PubMed]

Arslan, S.

B. Okumus, S. Arslan, S. M. Fengler, S. Myong, and T. Ha, “Single molecule nanocontainers made porous using a bacterial toxin,” J. Am. Chem. Soc. 131(41), 14844–14849 (2009).
[Crossref] [PubMed]

Baybayan, P.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Benítez, J. J.

J. J. Benítez, A. M. Keller, and P. Chen, “Nanovesicle trapping for studying weak protein interactions by single-molecule FRET,” Methods Enzymol. 472, 41–60 (2010).
[Crossref] [PubMed]

Bettman, B.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Bibillo, A.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Bjornson, K.

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M. Tokunaga, K. Kitamura, K. Saito, A. H. Iwane, and T. Yanagida, “Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy,” Biochem. Biophys. Res. Commun. 235(1), 47–53 (1997).
[Crossref] [PubMed]

T. Funatsu, Y. Harada, H. Higuchi, M. Tokunaga, K. Saito, Y. Ishii, R. D. Vale, and T. Yanagida, “Imaging and nano-manipulation of single biomolecules,” Biophys. Chem. 68(1-3), 63–72 (1997).
[Crossref] [PubMed]

Tomaney, A.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Travers, K.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Trentham, D. R.

K. Oiwa, J. F. Eccleston, M. Anson, M. Kikumoto, C. T. Davis, G. P. Reid, M. A. Ferenczi, J. E. Corrie, A. Yamada, H. Nakayama, and D. R. Trentham, “Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives,” Biophys. J. 78(6), 3048–3071 (2000).
[Crossref] [PubMed]

Trulson, M.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Turner, S.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Turner, S. W.

S. Uemura, C. E. Aitken, J. Korlach, B. A. Flusberg, S. W. Turner, and J. D. Puglisi, “Real-time tRNA transit on single translating ribosomes at codon resolution,” Nature 464(7291), 1012–1017 (2010).
[Crossref] [PubMed]

J. Korlach, P. J. Marks, R. L. Cicero, J. J. Gray, D. L. Murphy, D. B. Roitman, T. T. Pham, G. A. Otto, M. Foquet, and S. W. Turner, “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures,” Proc. Natl. Acad. Sci. U.S.A. 105(4), 1176–1181 (2008).
[Crossref] [PubMed]

M. J. Levene, J. Korlach, S. W. Turner, M. Foquet, H. G. Craighead, and W. W. Webb, “Zero-mode waveguides for single-molecule analysis at high concentrations,” Science 299(5607), 682–686 (2003).
[Crossref] [PubMed]

Uemura, S.

S. Uemura, C. E. Aitken, J. Korlach, B. A. Flusberg, S. W. Turner, and J. D. Puglisi, “Real-time tRNA transit on single translating ribosomes at codon resolution,” Nature 464(7291), 1012–1017 (2010).
[Crossref] [PubMed]

Vale, R. D.

T. Funatsu, Y. Harada, H. Higuchi, M. Tokunaga, K. Saito, Y. Ishii, R. D. Vale, and T. Yanagida, “Imaging and nano-manipulation of single biomolecules,” Biophys. Chem. 68(1-3), 63–72 (1997).
[Crossref] [PubMed]

van Oijen, A. M.

A. B. Loveland, S. Habuchi, J. C. Walter, and A. M. van Oijen, “A general approach to break the concentration barrier in single-molecule imaging,” Nat. Methods 9(10), 987–992 (2012).
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Vieceli, J.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
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Villa, E.

W. Qiu, N. D. Derr, B. S. Goodman, E. Villa, D. Wu, W. Shih, and S. L. Reck-Peterson, “Dynein achieves processive motion using both stochastic and coordinated stepping,” Nat. Struct. Mol. Biol. 19(2), 193–200 (2012).
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Walter, J. C.

A. B. Loveland, S. Habuchi, J. C. Walter, and A. M. van Oijen, “A general approach to break the concentration barrier in single-molecule imaging,” Nat. Methods 9(10), 987–992 (2012).
[Crossref] [PubMed]

Webb, M. R.

T. Sakamoto, M. R. Webb, E. Forgacs, H. D. White, and J. R. Sellers, “Direct observation of the mechanochemical coupling in myosin Va during processive movement,” Nature 455(7209), 128–132 (2008).
[Crossref] [PubMed]

Webb, W. W.

M. J. Levene, J. Korlach, S. W. Turner, M. Foquet, H. G. Craighead, and W. W. Webb, “Zero-mode waveguides for single-molecule analysis at high concentrations,” Science 299(5607), 682–686 (2003).
[Crossref] [PubMed]

Wegener, J.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Wenger, J.

White, H. D.

T. Sakamoto, M. R. Webb, E. Forgacs, H. D. White, and J. R. Sellers, “Direct observation of the mechanochemical coupling in myosin Va during processive movement,” Nature 455(7209), 128–132 (2008).
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Wu, D.

W. Qiu, N. D. Derr, B. S. Goodman, E. Villa, D. Wu, W. Shih, and S. L. Reck-Peterson, “Dynein achieves processive motion using both stochastic and coordinated stepping,” Nat. Struct. Mol. Biol. 19(2), 193–200 (2012).
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J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
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Yamada, A.

K. Oiwa, J. F. Eccleston, M. Anson, M. Kikumoto, C. T. Davis, G. P. Reid, M. A. Ferenczi, J. E. Corrie, A. Yamada, H. Nakayama, and D. R. Trentham, “Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives,” Biophys. J. 78(6), 3048–3071 (2000).
[Crossref] [PubMed]

Yanagida, T.

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, and T. Yanagida, “Simultaneous measurement of nucleotide occupancy and mechanical displacement in myosin-V, a processive molecular motor,” Biophys. J. 96(1), L04–L06 (2009).
[Crossref] [PubMed]

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, and T. Yanagida, “Measurement system for simultaneous observation of myosin V chemical and mechanical events,” Biosystems 93(1-2), 48–57 (2008).
[Crossref] [PubMed]

A. Ishijima, H. Kojima, T. Funatsu, M. Tokunaga, H. Higuchi, H. Tanaka, and T. Yanagida, “Simultaneous observation of individual ATPase and mechanical events by a single myosin molecule during interaction with actin,” Cell 92(2), 161–171 (1998).
[Crossref] [PubMed]

T. Funatsu, Y. Harada, H. Higuchi, M. Tokunaga, K. Saito, Y. Ishii, R. D. Vale, and T. Yanagida, “Imaging and nano-manipulation of single biomolecules,” Biophys. Chem. 68(1-3), 63–72 (1997).
[Crossref] [PubMed]

M. Tokunaga, K. Kitamura, K. Saito, A. H. Iwane, and T. Yanagida, “Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy,” Biochem. Biophys. Res. Commun. 235(1), 47–53 (1997).
[Crossref] [PubMed]

Yang, A.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Yang, Z.

H. L. Sweeney, H. Park, A. B. Zong, Z. Yang, P. R. Selvin, and S. S. Rosenfeld, “How myosin VI coordinates its heads during processive movement,” EMBO J. 26(11), 2682–2692 (2007).
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Yildiz, A.

M. A. DeWitt, A. Y. Chang, P. A. Combs, and A. Yildiz, “Cytoplasmic dynein moves through uncoordinated stepping of the AAA+ ring domains,” Science 335(6065), 221–225 (2012).
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Yoshida, M.

K. Adachi, K. Oiwa, T. Nishizaka, S. Furuike, H. Noji, H. Itoh, M. Yoshida, and K. Kinosita., “Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation,” Cell 130(2), 309–321 (2007).
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Zaccarin, D.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
[Crossref] [PubMed]

Zhao, P.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
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Zhong, F.

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner, “Real-time DNA sequencing from single polymerase molecules,” Science 323(5910), 133–138 (2009).
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Zong, A. B.

H. L. Sweeney, H. Park, A. B. Zong, Z. Yang, P. R. Selvin, and S. S. Rosenfeld, “How myosin VI coordinates its heads during processive movement,” EMBO J. 26(11), 2682–2692 (2007).
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Biochem. Biophys. Res. Commun. (1)

M. Tokunaga, K. Kitamura, K. Saito, A. H. Iwane, and T. Yanagida, “Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy,” Biochem. Biophys. Res. Commun. 235(1), 47–53 (1997).
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Biophys. Chem. (1)

T. Funatsu, Y. Harada, H. Higuchi, M. Tokunaga, K. Saito, Y. Ishii, R. D. Vale, and T. Yanagida, “Imaging and nano-manipulation of single biomolecules,” Biophys. Chem. 68(1-3), 63–72 (1997).
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S. M. Block, “Kinesin motor mechanics: binding, stepping, tracking, gating, and limping,” Biophys. J. 92(9), 2986–2995 (2007).
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K. Oiwa, J. F. Eccleston, M. Anson, M. Kikumoto, C. T. Davis, G. P. Reid, M. A. Ferenczi, J. E. Corrie, A. Yamada, H. Nakayama, and D. R. Trentham, “Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives,” Biophys. J. 78(6), 3048–3071 (2000).
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Biosystems (1)

T. Komori, S. Nishikawa, T. Ariga, A. H. Iwane, and T. Yanagida, “Measurement system for simultaneous observation of myosin V chemical and mechanical events,” Biosystems 93(1-2), 48–57 (2008).
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Cell (2)

K. Adachi, K. Oiwa, T. Nishizaka, S. Furuike, H. Noji, H. Itoh, M. Yoshida, and K. Kinosita., “Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation,” Cell 130(2), 309–321 (2007).
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EMBO J. (1)

H. L. Sweeney, H. Park, A. B. Zong, Z. Yang, P. R. Selvin, and S. S. Rosenfeld, “How myosin VI coordinates its heads during processive movement,” EMBO J. 26(11), 2682–2692 (2007).
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E. Boukobza, A. Sonnenfeld, and G. Haran, “Immobilization in Surface-Tethered Lipid Vesicles as a New Tool for Single Biomolecule Spectroscopy,” J. Phys. Chem. B 105(48), 12165–12170 (2001).
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A. B. Loveland, S. Habuchi, J. C. Walter, and A. M. van Oijen, “A general approach to break the concentration barrier in single-molecule imaging,” Nat. Methods 9(10), 987–992 (2012).
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Nat. Struct. Mol. Biol. (1)

W. Qiu, N. D. Derr, B. S. Goodman, E. Villa, D. Wu, W. Shih, and S. L. Reck-Peterson, “Dynein achieves processive motion using both stochastic and coordinated stepping,” Nat. Struct. Mol. Biol. 19(2), 193–200 (2012).
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Nature (2)

T. Sakamoto, M. R. Webb, E. Forgacs, H. D. White, and J. R. Sellers, “Direct observation of the mechanochemical coupling in myosin Va during processive movement,” Nature 455(7209), 128–132 (2008).
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S. Uemura, C. E. Aitken, J. Korlach, B. A. Flusberg, S. W. Turner, and J. D. Puglisi, “Real-time tRNA transit on single translating ribosomes at codon resolution,” Nature 464(7291), 1012–1017 (2010).
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Opt. Express (1)

Proc. Natl. Acad. Sci. U.S.A. (5)

J. Korlach, P. J. Marks, R. L. Cicero, J. J. Gray, D. L. Murphy, D. B. Roitman, T. T. Pham, G. A. Otto, M. Foquet, and S. W. Turner, “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures,” Proc. Natl. Acad. Sci. U.S.A. 105(4), 1176–1181 (2008).
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Figures (6)

Fig. 1
Fig. 1

Schematics of new microscopy methods demonstrated in this work that suppress background fluorescence. (a) Myosin walking on actin in a linear ZMW (not to scale). Fluorescent ATP molecules (red dots) are only excited when they are located very near the entrance to the ZMW. Since the ZMW slits are narrower than the wavelength of light, the excitation volume is confined both vertically and in the direction in which the slits are narrowest. (b) Myosin walking in the CLIC device (not to scale). Near the contact region, the thin CLIC imaging chamber confines the excited molecules to a thin layer.

Fig. 2
Fig. 2

Strategy for polymerizing actin in a linear ZMW (not to scale). Each panel shows a side view of the waveguide. Gray and white boxes indicate the aluminum film and glass coverslip, respectively. (a) Glass at the bottom of the waveguide is selectively functionalized with biotin, which is then covered with a layer of streptavidin. Next, short biotinylated actin filament “seeds” are sparsely added to the waveguide and bind to the bottom surface. (b) Non-biotinylated G-actin is added to the waveguide under salt conditions that allow polymerization, and polymerization occurs off of the seed filaments. The nascent filaments are not attached to the surface during the polymerization step. (c) Biotinylated phalloidin is added to the slide, pulling down the nascent filaments and attaching them to the bottom surface of the waveguide.

Fig. 3
Fig. 3

Flow-cell CLIC apparatus. (a) Side view of the flow-cell CLIC apparatus (not to scale). The lens (Thorlabs LA4966) is initially raised for sample insertion (left) and subsequently lowered for imaging (right), decreasing the volume of excited fluorophores (pink) in the imaging region. Excitation light entering from below is shown in green. (b) Top-view of the CLIC device (to scale). A cantilever controls the lens positioning. It contains a clearance hole for a finely threaded rod (Thorlabs F25US200). A spring (Small Parts CSXX-0160-05) is mounted around the rod and directly above the cantilever. A finely threaded lock-nut (Thorlabs LN25100) is mounted on the rod directly above the spring. The downward rotation of the lock-nut presses against the spring and consequently lowers the lens. The spring resists the downward motion of the lock-nut with approximately the same force (~1 N) as is required to deform the coverslip in this geometry. The initial flow chamber (~8 mm wide, ~100 µm thick) is confined vertically by the top and bottom coverslip surfaces and laterally by the edges of double-sided tape. The cantilever is mounted, using custom clamps, on a thin aluminum hinge aligned so that the lens surface is in contact with the top of the flow cell when the cantilever is horizontal. The flow cell is held in place by custom spring clips. (c) Side view of the CLIC device showing the imaging chamber (to scale). The dark gray trapezoid depicts a hole in the plate that gives clearance for the objective.

Fig. 4
Fig. 4

Linear ZMWs restrict fluorescent excitation when light is polarized parallel to the slits. (a) 2D finite-element time-domain simulations of excitation light intensity with polarization perpendicular to the long dimension of the waveguide. Simulations were performed for a 50 nm linear ZMW and the intensity is plotted on a log scale. Under this condition, a significant amount of excitation light propagates up into solution. (b) Simulations analogous to panel (a), but with excitation light polarization parallel to the long dimension of the waveguide (condition that minimizes background fluorescence). Under this condition, intensity has decreased by about 3 orders of magnitude over the 120 nm depth of the linear ZMW. Note that the log intensity scale varies between panels (a) and (b). (c) Image of nanofabricated linear ZMW, imaged with a 20x objective and a white light source. Linear ZMWs range from ~50-250 nm in width. The linear ZMW at the top of the image include manufacturing defects of unknown cause. The definition of the polarization angle for panels (a) and (b) is drawn on top of the image. (d) Average fluorescence intensity (red dots) due to the diffuse background of 1 µM free Cy3-ATP as a function of the excitation polarization angle with fit to theory (blue line). When the polarization is parallel to the longest dimension of the ZMW, the background fluorescence is minimized.

Fig. 5
Fig. 5

Example kymograph of myosin V molecules walking along actin in a linear ZMW. Note that in some of the myosin runs shown in this kymograph, such as the one beginning around 5 seconds and the one beginning around 35 seconds, two myosin molecules are walking along the actin filament very close together.

Fig. 6
Fig. 6

Processive myosin movement is observed under confinement in the flow-cell CLIC device. (a) Interferometry of and least-squares fit to the CLIC imaging chamber height profile. The first two labeled interference minima (blue rings) correspond to heights of 184 nm and 368 nm respectively. (b) Two example kymographs of myosin proteins imaged in the chamber at heights of ~80 nm. (c) Distribution of the number of myosins exhibiting processive motion as a function of chamber height, normalized by area. Error bars represent the expected standard deviation assuming Poissonian counting statistics. (d) Scatter plot of processive motor speed vs. chamber height. The speed shows little correlation with chamber height, indicating that confinement does not significantly perturb the motor behavior at heights where motors continue to walk.

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