-
1
-
-
77649111696
-
Insights into the sliding movement of the lac repressor nonspecifically bound to DNA
-
Furini, S.; Domene, C.; Cavalcanti, S. Insights into the sliding movement of the lac repressor nonspecifically bound to DNA. J. Phys. Chem. B 2010, 114, 2238-2245.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2238-2245
-
-
Furini, S.1
Domene, C.2
Cavalcanti, S.3
-
2
-
-
33846078626
-
REBASE-Enzymes and genes for DNA restriction and modification
-
Roberts, R.J.; Vincze, T.; Posfai, J.; Macelis, D. REBASE-Enzymes and genes for DNA restriction and modification. Nucleic Acids Res. 2007, 35, D269-D270.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
McElis, D.4
-
3
-
-
0024531901
-
Facilitated target location in biological systems
-
Von Hippel, P.H.; Berg, O.G. Facilitated target location in biological systems. J. Biol. Chem. 1989, 264, 675-678.
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 675-678
-
-
Von Hippel, P.H.1
Berg, O.G.2
-
5
-
-
48249095613
-
Single-molecule approach to molecular biology in living bacterial cells
-
Xie, X.S.; Choi, P.J.; Li, G.W.; Lee, N.K.; Lia, G. Single-molecule approach to molecular biology in living bacterial cells. Annu. Rev. Biophys. 2008, 37, 417-444.
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 417-444
-
-
Xie, X.S.1
Choi, P.J.2
Li, G.W.3
Lee, N.K.4
Lia, G.5
-
6
-
-
3042579602
-
How do site-specific DNA-binding proteins find their targets?
-
Halford, S.E.; Marko, J.F. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 2004, 32, 3040-3052.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3040-3052
-
-
Halford, S.E.1
Marko, J.F.2
-
7
-
-
0035140806
-
High local protein concentrations at promoters: Strategies in prokaryotic and eukaryotic cells
-
Droge, P.; Muller-Hill, B. High local protein concentrations at promoters: Strategies in prokaryotic and eukaryotic cells. Bioessays 2001, 23, 179-183.
-
(2001)
Bioessays
, vol.23
, pp. 179-183
-
-
Droge, P.1
Muller-Hill, B.2
-
8
-
-
84860440982
-
Intra-nuclear mobility and target search mechanisms of transcription factors: A single-molecule perspective on gene expression
-
Normanno, D.; Dahan, M.; Darzacq, X. Intra-nuclear mobility and target search mechanisms of transcription factors: A single-molecule perspective on gene expression. Biochim. Biophys. Acta 2012, 1819, 482-493.
-
(2012)
Biochim. Biophys. Acta
, vol.1819
, pp. 482-493
-
-
Normanno, D.1
Dahan, M.2
Darzacq, X.3
-
9
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
Jacob, F.; Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 1961, 3, 318-356.
-
(1961)
J. Mol. Biol.
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
10
-
-
0014945567
-
The lac repressor-operator interaction. 3. Kinetic studies
-
Riggs, A.D.; Bourgeois, S.; Cohn, M. The lac repressor-operator interaction. 3. Kinetic studies. J. Mol. Biol. 1970, 53, 401-417.
-
(1970)
J. Mol. Biol.
, vol.53
, pp. 401-417
-
-
Riggs, A.D.1
Bourgeois, S.2
Cohn, M.3
-
11
-
-
0036468995
-
Kinetic studies of protein-protein interactions
-
Schreiber, G. Kinetic studies of protein-protein interactions. Curr. Opin. Struct. Biol. 2002, 12, 41-47.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 41-47
-
-
Schreiber, G.1
-
12
-
-
0016302334
-
Diffusion controlled reaction rates in spheroidal geometry. Application to repressor-operator association and membrane bound enzymes
-
Richter, P.H.; Eigen, M. Diffusion controlled reaction rates in spheroidal geometry. Application to repressor-operator association and membrane bound enzymes. Biophys. Chem. 1974, 2, 255-263.
-
(1974)
Biophys. Chem.
, vol.2
, pp. 255-263
-
-
Richter, P.H.1
Eigen, M.2
-
14
-
-
72149127671
-
How a protein searches for its site on DNA: The mechanism of facilitated diffusion
-
Mirny, L.; Slutsky, M.; Wunderlich, Z.; Tafvizi, A.; Leith, J.; Kosmrlj, A. How a protein searches for its site on DNA: The mechanism of facilitated diffusion. J. Phys. A 2009, 42, 434013.
-
(2009)
J. Phys. A
, vol.42
, pp. 434013
-
-
Mirny, L.1
Slutsky, M.2
Wunderlich, Z.3
Tafvizi, A.4
Leith, J.5
Kosmrlj, A.6
-
15
-
-
65549171477
-
An end to 40 years of mistakes in DNA-protein association kinetics?
-
Halford, S.E. An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans. 2009, 37, 343-348.
-
(2009)
Biochem. Soc. Trans.
, vol.37
, pp. 343-348
-
-
Halford, S.E.1
-
16
-
-
0020123756
-
Association kinetics with coupled three-and one-dimensional diffusion. Chain-length dependence of the association rate of specific DNA sites
-
Berg, O.G.; Ehrenberg, M. Association kinetics with coupled three-and one-dimensional diffusion. Chain-length dependence of the association rate of specific DNA sites. Biophys. Chem. 1982, 15, 41-51.
-
(1982)
Biophys. Chem.
, vol.15
, pp. 41-51
-
-
Berg, O.G.1
Ehrenberg, M.2
-
17
-
-
0019887628
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
-
Berg, O.G.; Winter, R.B.; von Hippel, P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 1981, 20, 6929-6948.
-
(1981)
Biochemistry
, vol.20
, pp. 6929-6948
-
-
Berg, O.G.1
Winter, R.B.2
von Hippel, P.H.3
-
18
-
-
0019867850
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: Kinetic measurements and conclusions
-
Winter, R.B.; Berg, O.G.; von Hippel, P.H. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interaction: Kinetic measurements and conclusions. Biochemistry 1981, 20, 6961-6977.
-
(1981)
Biochemistry
, vol.20
, pp. 6961-6977
-
-
Winter, R.B.1
Berg, O.G.2
von Hippel, P.H.3
-
19
-
-
0018165783
-
Association kinetics with coupled diffusion III. Ionic-strength dependence of the lac repressor-operator association
-
Berg, O.G.; Blomberg, C. Association kinetics with coupled diffusion III. Ionic-strength dependence of the lac repressor-operator association. Biophys. Chem. 1978, 8, 271-280.
-
(1978)
Biophys. Chem.
, vol.8
, pp. 271-280
-
-
Berg, O.G.1
Blomberg, C.2
-
20
-
-
0017388544
-
Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the lac repressor-operator system
-
Berg, O.G.; Blomberg, C. Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the lac repressor-operator system. Biophys. Chem. 1977, 7, 33-39.
-
(1977)
Biophys. Chem.
, vol.7
, pp. 33-39
-
-
Berg, O.G.1
Blomberg, C.2
-
21
-
-
0017143653
-
Association kinetics with coupled diffusional flows. Special application to the lac repressor-operator system
-
Berg, O.G.; Blomberg, C. Association kinetics with coupled diffusional flows. Special application to the lac repressor-operator system. Biophys. Chem. 1976, 4, 367-381.
-
(1976)
Biophys. Chem.
, vol.4
, pp. 367-381
-
-
Berg, O.G.1
Blomberg, C.2
-
22
-
-
84862624197
-
The lac repressor displays facilitated diffusion in living cells
-
Hammar, P.; Leroy, P.; Mahmutovic, A.; Marklund, E.G.; Berg, O.G.; Elf, J. The lac repressor displays facilitated diffusion in living cells. Science 2012, 336, 1595-1598.
-
(2012)
Science
, vol.336
, pp. 1595-1598
-
-
Hammar, P.1
Leroy, P.2
Mahmutovic, A.3
Marklund, E.G.4
Berg, O.G.5
Elf, J.6
-
23
-
-
10044223573
-
Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
-
Slutsky, M.; Mirny, L.A. Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophys. J. 2004, 87, 4021-4035.
-
(2004)
Biophys. J.
, vol.87
, pp. 4021-4035
-
-
Slutsky, M.1
Mirny, L.A.2
-
24
-
-
33746649820
-
Single molecule measurements of repressor protein 1D diffusion on DNA
-
Wang, Y.M.; Austin, R.H.; Cox, E.C. Single molecule measurements of repressor protein 1D diffusion on DNA. Phys. Rev. Lett. 2006, 97, 048302.
-
(2006)
Phys. Rev. Lett.
, vol.97
, pp. 048302
-
-
Wang, Y.M.1
Austin, R.H.2
Cox, E.C.3
-
25
-
-
0026659283
-
How Lac repressor finds lac operator in vitro
-
Fickert, R.; Muller-Hill, B. How Lac repressor finds lac operator in vitro. J. Mol. Biol. 1992, 226, 59-68.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 59-68
-
-
Fickert, R.1
Muller-Hill, B.2
-
26
-
-
2342640588
-
Enzyme-mediated DNA looping
-
Halford, S.E.; Welsh, A.J.; Szczelkun, M.D. Enzyme-mediated DNA looping. Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 1-24.
-
(2004)
Annu. Rev. Biophys. Biomol. Struct.
, vol.33
, pp. 1-24
-
-
Halford, S.E.1
Welsh, A.J.2
Szczelkun, M.D.3
-
27
-
-
49449107340
-
Visualizing one-dimensional diffusion of proteins along DNA
-
Gorman, J.; Greene, E.C. Visualizing one-dimensional diffusion of proteins along DNA. Nat. Struct. Mol. Biol. 2008, 15, 768-774.
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 768-774
-
-
Gorman, J.1
Greene, E.C.2
-
28
-
-
50649105347
-
In singulo biochemistry: When less is more
-
Bustamante, C. In singulo biochemistry: When less is more. Annu. Rev. Biochem. 2008, 77, 45-50.
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 45-50
-
-
Bustamante, C.1
-
29
-
-
79959655626
-
Biological mechanisms, one molecule at a time
-
Tinoco, I., Jr.; Gonzalez, R.L., Jr. Biological mechanisms, one molecule at a time. Genes Dev. 2011, 25, 1205-1231.
-
(2011)
Genes Dev.
, vol.25
, pp. 1205-1231
-
-
Tinoco Jr., I.1
Gonzalez Jr., R.L.2
-
30
-
-
14144255434
-
Exploring molecular motors and switches at the single-molecule level
-
Capitanio, M.; Vanzi, F.; Broggio, C.; Cicchi, R.; Normanno, D.; Romano, G.; Sacconi, L.; Pavone, F.S. Exploring molecular motors and switches at the single-molecule level. Microsc. Res. Tech. 2004, 65, 194-204.
-
(2004)
Microsc. Res. Tech.
, vol.65
, pp. 194-204
-
-
Capitanio, M.1
Vanzi, F.2
Broggio, C.3
Cicchi, R.4
Normanno, D.5
Romano, G.6
Sacconi, L.7
Pavone, F.S.8
-
31
-
-
34347240880
-
New fluorescent tools for watching nanometer-scale conformational changes of single molecules
-
Toprak, E.; Selvin, P.R. New fluorescent tools for watching nanometer-scale conformational changes of single molecules. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 349-369.
-
(2007)
Annu. Rev. Biophys. Biomol. Struct.
, vol.36
, pp. 349-369
-
-
Toprak, E.1
Selvin, P.R.2
-
32
-
-
0025867008
-
Transcription by single molecules of RNA polymerase observed by light microscopy
-
Schafer, D.A.; Gelles, J.; Sheetz, M.P.; Landick, R. Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 1991, 352, 444-448.
-
(1991)
Nature
, vol.352
, pp. 444-448
-
-
Schafer, D.A.1
Gelles, J.2
Sheetz, M.P.3
Landick, R.4
-
33
-
-
0028143652
-
Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule
-
Yin, H.; Landick, R.; Gelles, J. Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule. Biophys. J. 1994, 67, 2468-2478.
-
(1994)
Biophys. J.
, vol.67
, pp. 2468-2478
-
-
Yin, H.1
Landick, R.2
Gelles, J.3
-
35
-
-
2442673068
-
Single-particle tracking for DNA tether length monitoring
-
Pouget, N.; Dennis, C.; Turlan, C.; Grigoriev, M.; Chandler, M.; Salome, L. Single-particle tracking for DNA tether length monitoring. Nucleic Acids Res. 2004, 32, e73.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Pouget, N.1
Dennis, C.2
Turlan, C.3
Grigoriev, M.4
Chandler, M.5
Salome, L.6
-
36
-
-
23244442263
-
Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy
-
Blumberg, S.; Gajraj, A.; Pennington, M.W.; Meiners, J.C. Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy. Biophys. J. 2005, 89, 1272-1281.
-
(2005)
Biophys. J.
, vol.89
, pp. 1272-1281
-
-
Blumberg, S.1
Gajraj, A.2
Pennington, M.W.3
Meiners, J.C.4
-
37
-
-
80455149889
-
Tethered particle motion mediated by scattering from gold nanoparticles and darkfield microscopy
-
doi:10.1117/1.3174445
-
Dietrich, H.R.C.; Rieger, B.; Wiertz, F.G.M.; de Groote, F.H.; Heering, H.A.; Young, I.T.; Garini, Y. Tethered particle motion mediated by scattering from gold nanoparticles and darkfield microscopy. J. Nanophotonics 2009, 3, doi:10.1117/1.3174445.
-
(2009)
J. Nanophotonics
, vol.3
-
-
Dietrich, H.R.C.1
Rieger, B.2
Wiertz, F.G.M.3
de Groote, F.H.4
Heering, H.A.5
Young, I.T.6
Garini, Y.7
-
38
-
-
33746207766
-
Lac repressor hinge flexibility and DNA looping: Single molecule kinetics by tethered particle motion
-
Vanzi, F.; Broggio, C.; Sacconi, L.; Pavone, F.S. Lac repressor hinge flexibility and DNA looping: Single molecule kinetics by tethered particle motion. Nucleic Acids Res. 2006, 34, 3409-3420.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3409-3420
-
-
Vanzi, F.1
Broggio, C.2
Sacconi, L.3
Pavone, F.S.4
-
39
-
-
31544452261
-
Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
-
Van den Broek, B.; Vanzi, F.; Normanno, D.; Pavone, F.S.; Wuite, G.J. Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res. 2006, 34, 167-174.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 167-174
-
-
Van den Broek, B.1
Vanzi, F.2
Normanno, D.3
Pavone, F.S.4
Wuite, G.J.5
-
40
-
-
0028956979
-
Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules
-
Finzi, L.; Gelles, J. Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science 1995, 267, 378-380.
-
(1995)
Science
, vol.267
, pp. 378-380
-
-
Finzi, L.1
Gelles, J.2
-
41
-
-
70349748589
-
Tetramer opening in LacI-mediated DNA looping
-
Rutkauskas, D.; Zhan, H.L.; Matthews, K.S.; Pavone, F.S.; Vanzi, F. Tetramer opening in LacI-mediated DNA looping. Proc. Natl. Acad. Sci. USA 2009, 106, 16627-16632.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 16627-16632
-
-
Rutkauskas, D.1
Zhan, H.L.2
Matthews, K.S.3
Pavone, F.S.4
Vanzi, F.5
-
42
-
-
66249118030
-
Concentration and length dependence of DNA looping in transcriptional regulation
-
Han, L.; Garcia, H.G.; Blumberg, S.; Towles, K.B.; Beausang, J.F.; Nelson, P.C.; Phillips, R. Concentration and length dependence of DNA looping in transcriptional regulation. PLoS One 2009, 4, e5621.
-
(2009)
PLoS One
, vol.4
-
-
Han, L.1
Garcia, H.G.2
Blumberg, S.3
Towles, K.B.4
Beausang, J.F.5
Nelson, P.C.6
Phillips, R.7
-
43
-
-
54749084305
-
Interconvertible lac repressor-DNA loops revealed by single-molecule experiments
-
Wong, O.K.; Guthold, M.; Erie, D.A.; Gelles, J. Interconvertible lac repressor-DNA loops revealed by single-molecule experiments. PLoS Biol. 2008, 6, e232.
-
(2008)
PLoS Biol.
, vol.6
-
-
Wong, O.K.1
Guthold, M.2
Erie, D.A.3
Gelles, J.4
-
44
-
-
84870573112
-
Sequence dependence of transcription factor-mediated DNA looping
-
Johnson, S.; Linden, M.; Phillips, R. Sequence dependence of transcription factor-mediated DNA looping. Nucleic Acids Res. 2012, 40, 7728-7738.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 7728-7738
-
-
Johnson, S.1
Linden, M.2
Phillips, R.3
-
45
-
-
77954095767
-
Protein-mediated DNA loop formation and breakdown in a fluctuating environment
-
Chen, Y.F.; Milstein, J.N.; Meiners, J.C. Protein-mediated DNA loop formation and breakdown in a fluctuating environment. Phys. Rev. Lett. 2010, 104, 258103.
-
(2010)
Phys. Rev. Lett.
, vol.104
, pp. 258103
-
-
Chen, Y.F.1
Milstein, J.N.2
Meiners, J.C.3
-
46
-
-
75849124054
-
Femtonewton entropic forces can control the formation of protein-mediated DNA loops
-
Chen, Y.F.; Milstein, J.N.; Meiners, J.C. Femtonewton entropic forces can control the formation of protein-mediated DNA loops. Phys. Rev. Lett. 2010, 104, 048301.
-
(2010)
Phys. Rev. Lett.
, vol.104
, pp. 048301
-
-
Chen, Y.F.1
Milstein, J.N.2
Meiners, J.C.3
-
47
-
-
33750007449
-
IS911 transpososome assembly as analysed by tethered particle motion
-
Pouget, N.; Turlan, C.; Destainville, N.; Salome, L.; Chandler, M. IS911 transpososome assembly as analysed by tethered particle motion. Nucleic Acids Res. 2006, 34, 4313-4323.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 4313-4323
-
-
Pouget, N.1
Turlan, C.2
Destainville, N.3
Salome, L.4
Chandler, M.5
-
48
-
-
66249111861
-
Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor
-
Zurla, C.; Manzo, C.; Dunlap, D.; Lewis, D.E.; Adhya, S.; Finzi, L. Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. Nucleic Acids Res. 2009, 37, 2789-2795.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2789-2795
-
-
Zurla, C.1
Manzo, C.2
Dunlap, D.3
Lewis, D.E.4
Adhya, S.5
Finzi, L.6
-
49
-
-
84867644247
-
The effect of nonspecific binding of lambda repressor on DNA looping dynamics
-
Manzo, C.; Zurla, C.; Dunlap, D.D.; Finzi, L. The effect of nonspecific binding of lambda repressor on DNA looping dynamics. Biophys. J. 2012, 103, 1753-1761.
-
(2012)
Biophys. J.
, vol.103
, pp. 1753-1761
-
-
Manzo, C.1
Zurla, C.2
Dunlap, D.D.3
Finzi, L.4
-
50
-
-
84862178413
-
DNA looping by FokI: The impact of twisting and bending rigidity on protein-induced looping dynamics
-
Laurens, N.; Rusling, D.A.; Pernstich, C.; Brouwer, I.; Halford, S.E.; Wuite, G.J. DNA looping by FokI: The impact of twisting and bending rigidity on protein-induced looping dynamics. Nucleic Acids Res. 2012, 40, 4988-4997.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 4988-4997
-
-
Laurens, N.1
Rusling, D.A.2
Pernstich, C.3
Brouwer, I.4
Halford, S.E.5
Wuite, G.J.6
-
51
-
-
33646168041
-
Stepwise bending of DNA by a single TATA-box binding protein
-
Tolic-Norrelykke, S.F.; Rasmussen, M.B.; Pavone, F.S.; Berg-Sorensen, K.; Oddershede, L.B. Stepwise bending of DNA by a single TATA-box binding protein. Biophys. J. 2006, 90, 3694-3703.
-
(2006)
Biophys. J.
, vol.90
, pp. 3694-3703
-
-
Tolic-Norrelykke, S.F.1
Rasmussen, M.B.2
Pavone, F.S.3
Berg-Sorensen, K.4
Oddershede, L.B.5
-
52
-
-
33749359386
-
Viewing single lambda site-specific recombination events from start to finish
-
Mumm, J.P.; Landy, A.; Gelles, J. Viewing single lambda site-specific recombination events from start to finish. EMBO J. 2006, 25, 4586-4595.
-
(2006)
EMBO J.
, vol.25
, pp. 4586-4595
-
-
Mumm, J.P.1
Landy, A.2
Gelles, J.3
-
53
-
-
84864482180
-
Real-time single-molecule tethered particle motion experiments reveal the kinetics and mechanisms of Cre-mediated site-specific recombination
-
Fan, H.F. Real-time single-molecule tethered particle motion experiments reveal the kinetics and mechanisms of Cre-mediated site-specific recombination. Nucleic Acids Res. 2012, 40, 6208-6222.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 6208-6222
-
-
Fan, H.F.1
-
54
-
-
65549152342
-
Studying RecBCD helicase translocation along chi-DNA using tethered particle motion with a stretching force
-
Fan, H.F.; Li, H.W. Studying RecBCD helicase translocation along chi-DNA using tethered particle motion with a stretching force. Biophys. J. 2009, 96, 1875-1883.
-
(2009)
Biophys. J.
, vol.96
, pp. 1875-1883
-
-
Fan, H.F.1
Li, H.W.2
-
55
-
-
84870570253
-
High-throughput single-molecule analysis of DNA-protein interactions by tethered particle motion
-
Plenat, T.; Tardin, C.; Rousseau, P.; Salome, L. High-throughput single-molecule analysis of DNA-protein interactions by tethered particle motion. Nucleic Acids Res. 2012, 40, e89.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Plenat, T.1
Tardin, C.2
Rousseau, P.3
Salome, L.4
-
56
-
-
79551504946
-
Probing DNA conformational changes with high temporal resolution by tethered particle motion
-
Manghi, M.; Tardin, C.; Baglio, J.; Rousseau, P.; Salome, L.; Destainville, N. Probing DNA conformational changes with high temporal resolution by tethered particle motion. Phys. Boil. 2010, 7, 046003.
-
(2010)
Phys. Boil.
, vol.7
, pp. 046003
-
-
Manghi, M.1
Tardin, C.2
Baglio, J.3
Rousseau, P.4
Salome, L.5
Destainville, N.6
-
57
-
-
34147143884
-
DNA looping kinetics analyzed using diffusive hidden Markov model
-
Beausang, J.F.; Zurla, C.; Manzo, C.; Dunlap, D.; Finzi, L.; Nelson, P.C. DNA looping kinetics analyzed using diffusive hidden Markov model. Biophys. J. 2007, 92, L64-L66.
-
(2007)
Biophys. J.
, vol.92
-
-
Beausang, J.F.1
Zurla, C.2
Manzo, C.3
Dunlap, D.4
Finzi, L.5
Nelson, P.C.6
-
58
-
-
77954571156
-
Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments
-
Manzo, C.; Finzi, L. Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments. Methods Enzymol. 2010, 475, 199-220.
-
(2010)
Methods Enzymol.
, vol.475
, pp. 199-220
-
-
Manzo, C.1
Finzi, L.2
-
59
-
-
34447267932
-
Analysis of kinetics in noisy systems: Application to single molecule tethered particle motion
-
Vanzi, F.; Sacconi, L.; Pavone, F.S. Analysis of kinetics in noisy systems: Application to single molecule tethered particle motion. Biophys. J. 2007, 93, 21-36.
-
(2007)
Biophys. J.
, vol.93
, pp. 21-36
-
-
Vanzi, F.1
Sacconi, L.2
Pavone, F.S.3
-
60
-
-
33644676435
-
Volume-exclusion effects in tethered-particle experiments: Bead size matters
-
Segall, D.E.; Nelson, P.C.; Phillips, R. Volume-exclusion effects in tethered-particle experiments: Bead size matters. Phys. Rev. Lett. 2006, 96, 088306:1-088306:4.
-
(2006)
Phys. Rev. Lett.
, vol.96
-
-
Segall, D.E.1
Nelson, P.C.2
Phillips, R.3
-
61
-
-
78649640916
-
Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments
-
Milstein, J.N.; Chen, Y.F.; Meiners, J.C. Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments. Biopolymers 2011, 95, 144-150.
-
(2011)
Biopolymers
, vol.95
, pp. 144-150
-
-
Milstein, J.N.1
Chen, Y.F.2
Meiners, J.C.3
-
62
-
-
0022655537
-
Observation of a single-beam gradient force optical trap for dielectric particles
-
Ashkin, A.; Dziedzic, J.M.; Bjorkholm, J.E.; Chu, S. Observation of a single-beam gradient force optical trap for dielectric particles. Opt. Lett. 1986, 11, 288-290.
-
(1986)
Opt. Lett.
, vol.11
, pp. 288-290
-
-
Ashkin, A.1
Dziedzic, J.M.2
Bjorkholm, J.E.3
Chu, S.4
-
63
-
-
0041967046
-
A revolution in optical manipulation
-
Grier, D.G. A revolution in optical manipulation. Nature 2003, 424, 810-816.
-
(2003)
Nature
, vol.424
, pp. 810-816
-
-
Grier, D.G.1
-
65
-
-
70449632886
-
High-resolution optical tweezers for investigating DNA-binding/translocating molecular motors
-
740007 doi:10.1117/12.826470
-
Wallin, A.E.; Ojala, H.; Ziedaite, G.; Degerth, L.; Bamford, D.; Haeggström, E. High-resolution optical tweezers for investigating DNA-binding/translocating molecular motors. Proc. SPIE 2009, 740007, doi:10.1117/12.826470.
-
(2009)
Proc. SPIE
-
-
Wallin, A.E.1
Ojala, H.2
Ziedaite, G.3
Degerth, L.4
Bamford, D.5
Haeggström, E.6
-
66
-
-
0032582494
-
Force and velocity measured for single molecules of RNA polymerase
-
Wang, M.D.; Schnitzer, M.J.; Yin, H.; Landick, R.; Gelles, J.; Block, S.M. Force and velocity measured for single molecules of RNA polymerase. Science 1998, 282, 902-907.
-
(1998)
Science
, vol.282
, pp. 902-907
-
-
Wang, M.D.1
Schnitzer, M.J.2
Yin, H.3
Landick, R.4
Gelles, J.5
Block, S.M.6
-
67
-
-
33745965527
-
Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing
-
Dalal, R.V.; Larson, M.H.; Neuman, K.C.; Gelles, J.; Landick, R.; Block, S.M. Pulling on the nascent RNA during transcription does not alter kinetics of elongation or ubiquitous pausing. Mol. Cell 2006, 23, 231-239.
-
(2006)
Mol. Cell
, vol.23
, pp. 231-239
-
-
Dalal, R.V.1
Larson, M.H.2
Neuman, K.C.3
Gelles, J.4
Landick, R.5
Block, S.M.6
-
68
-
-
6944221433
-
RNA polymerase can track a DNA groove during promoter search
-
Sakata-Sogawa, K.; Shimamoto, N. RNA polymerase can track a DNA groove during promoter search. Proc. Natl. Acad. Sci. USA 2004, 101, 14731-14735.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 14731-14735
-
-
Sakata-Sogawa, K.1
Shimamoto, N.2
-
69
-
-
0141499886
-
Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA
-
Koch, S.J.; Wang, M.D. Dynamic force spectroscopy of protein-DNA interactions by unzipping DNA. Phys. Rev. Lett. 2003, 91, 028103.
-
(2003)
Phys. Rev. Lett.
, vol.91
, pp. 028103
-
-
Koch, S.J.1
Wang, M.D.2
-
70
-
-
0030699999
-
Mechanical separation of the complementary strands of DNA
-
Essevaz-Roulet, B.; Bockelmann, U.; Heslot, F. Mechanical separation of the complementary strands of DNA. Proc. Natl. Acad. Sci. USA 1997, 94, 11935-11940.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 11935-11940
-
-
Essevaz-Roulet, B.1
Bockelmann, U.2
Heslot, F.3
-
71
-
-
0001767132
-
Molecular stick-slip motion revealed by opening DNA with piconewton forces
-
Bockelmann, U.; EssevazRoulet, B.; Heslot, F. Molecular stick-slip motion revealed by opening DNA with piconewton forces. Phys. Rev. Lett. 1997, 79, 4489-4492.
-
(1997)
Phys. Rev. Lett.
, vol.79
, pp. 4489-4492
-
-
Bockelmann, U.1
EssevazRoulet, B.2
Heslot, F.3
-
72
-
-
0035997065
-
Probing protein-DNA interactions by unzipping a single DNA double helix
-
Koch, S.J.; Shundrovsky, A.; Jantzen, B.C.; Wang, M.D. Probing protein-DNA interactions by unzipping a single DNA double helix. Biophys. J. 2002, 83, 1098-1105.
-
(2002)
Biophys. J.
, vol.83
, pp. 1098-1105
-
-
Koch, S.J.1
Shundrovsky, A.2
Jantzen, B.C.3
Wang, M.D.4
-
73
-
-
28444499354
-
Detection of high-affinity and sliding clamp modes for MSH2-MSH6 by single-molecule unzipping force analysis
-
Jiang, J.; Bai, L.; Surtees, J.A.; Gemici, Z.; Wang, M.D.; Alani, E. Detection of high-affinity and sliding clamp modes for MSH2-MSH6 by single-molecule unzipping force analysis. Mol. Cell 2005, 20, 771-781.
-
(2005)
Mol. Cell
, vol.20
, pp. 771-781
-
-
Jiang, J.1
Bai, L.2
Surtees, J.A.3
Gemici, Z.4
Wang, M.D.5
Alani, E.6
-
74
-
-
59649112972
-
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome
-
Hall, M.A.; Shundrovsky, A.; Bai, L.; Fulbright, R.M.; Lis, J.T.; Wang, M.D. High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nat. Struct. Mol. Biol. 2009, 16, 124-129.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 124-129
-
-
Hall, M.A.1
Shundrovsky, A.2
Bai, L.3
Fulbright, R.M.4
Lis, J.T.5
Wang, M.D.6
-
75
-
-
34250766751
-
Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase
-
Johnson, D.S.; Bai, L.; Smith, B.Y.; Patel, S.S.; Wang, M.D. Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell 2007, 129, 1299-1309.
-
(2007)
Cell
, vol.129
, pp. 1299-1309
-
-
Johnson, D.S.1
Bai, L.2
Smith, B.Y.3
Patel, S.S.4
Wang, M.D.5
-
76
-
-
80053897431
-
ATP-induced helicase slippage reveals highly coordinated subunits
-
Sun, B.; Johnson, D.S.; Patel, G.; Smith, B.Y.; Pandey, M.; Patel, S.S.; Wang, M.D. ATP-induced helicase slippage reveals highly coordinated subunits. Nature 2011, 478, 132-135.
-
(2011)
Nature
, vol.478
, pp. 132-135
-
-
Sun, B.1
Johnson, D.S.2
Patel, G.3
Smith, B.Y.4
Pandey, M.5
Patel, S.S.6
Wang, M.D.7
-
77
-
-
0141534308
-
Sequence-dependent pausing of single lambda exonuclease molecules
-
Perkins, T.T.; Dalal, R.V.; Mitsis, P.G.; Block, S.M. Sequence-dependent pausing of single lambda exonuclease molecules. Science 2003, 301, 1914-1918.
-
(2003)
Science
, vol.301
, pp. 1914-1918
-
-
Perkins, T.T.1
Dalal, R.V.2
Mitsis, P.G.3
Block, S.M.4
-
78
-
-
1542375262
-
Forward and reverse motion of single RecBCD molecules on DNA
-
Perkins, T.T.; Li, H.W.; Dalal, R.V.; Gelles, J.; Block, S.M. Forward and reverse motion of single RecBCD molecules on DNA. Biophys. J. 2004, 86, 1640-1648.
-
(2004)
Biophys. J.
, vol.86
, pp. 1640-1648
-
-
Perkins, T.T.1
Li, H.W.2
Dalal, R.V.3
Gelles, J.4
Block, S.M.5
-
79
-
-
0037133348
-
Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA
-
Brower-Toland, B.D.; Smith, C.L.; Yeh, R.C.; Lis, J.T.; Peterson, C.L.; Wang, M.D. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc. Natl. Acad. Sci. USA 2002, 99, 1960-1965.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1960-1965
-
-
Brower-Toland, B.D.1
Smith, C.L.2
Yeh, R.C.3
Lis, J.T.4
Peterson, C.L.5
Wang, M.D.6
-
80
-
-
33846411048
-
Continuous and time-shared multiple optical tweezers for the study of single motor proteins
-
Capitanio, M.; Cicchi, R.; Saverio Pavone, F. Continuous and time-shared multiple optical tweezers for the study of single motor proteins. Opt. Lasers Eng. 2007, 45, 450-457.
-
(2007)
Opt. Lasers Eng.
, vol.45
, pp. 450-457
-
-
Capitanio, M.1
Cicchi, R.2
Saverio Pavone, F.3
-
81
-
-
0030358936
-
Construction of multiple-beam optical traps with nanometer-resolution position sensing
-
Visscher, K.; Gross, S.P.; Block, S.M. Construction of multiple-beam optical traps with nanometer-resolution position sensing. IEEE J. Sel. Top. Quantum Electron. 1996, 2, 1066-1076.
-
(1996)
IEEE J. Sel. Top. Quantum Electron.
, vol.2
, pp. 1066-1076
-
-
Visscher, K.1
Gross, S.P.2
Block, S.M.3
-
82
-
-
23844475823
-
Position control and optical manipulation for nanotechnology applications
-
Capitanio, M.; Cicchi, R.; Pavone, F.S. Position control and optical manipulation for nanotechnology applications. Eur. Phys. J. B 2005, 46, 1-8.
-
(2005)
Eur. Phys. J. B
, vol.46
, pp. 1-8
-
-
Capitanio, M.1
Cicchi, R.2
Pavone, F.S.3
-
83
-
-
33847281331
-
Stabilization of an optical microscope to 0.1 nm in three dimensions
-
Carter, A.R.; King, G.M.; Ulrich, T.A.; Halsey, W.; Alchenberger, D.; Perkins, T.T. Stabilization of an optical microscope to 0.1 nm in three dimensions. Appl. Opt. 2007, 46, 421-427.
-
(2007)
Appl. Opt.
, vol.46
, pp. 421-427
-
-
Carter, A.R.1
King, G.M.2
Ulrich, T.A.3
Halsey, W.4
Alchenberger, D.5
Perkins, T.T.6
-
84
-
-
0036541291
-
Calibration of optical tweezers with differential interference contrast signals
-
Capitanio, M.; Romano, G.; Ballerini, R.; Giuntini, M.; Pavone, F.S.; Dunlap, D.; Finzi, L. Calibration of optical tweezers with differential interference contrast signals. Rev. Sci. Instrum. 2002, 73, 1687-1696.
-
(2002)
Rev. Sci. Instrum.
, vol.73
, pp. 1687-1696
-
-
Capitanio, M.1
Romano, G.2
Ballerini, R.3
Giuntini, M.4
Pavone, F.S.5
Dunlap, D.6
Finzi, L.7
-
85
-
-
33750527817
-
Calibration of optical tweezers with positional detection in the back focal plane
-
Tolic-Norrelykke, S.F.; Schaffer, E.; Howard, J.; Pavone, F.S.; Julicher, F.; Flyvbjerg, H. Calibration of optical tweezers with positional detection in the back focal plane. Rev. Sci. Instrum. 2006, 77, 103101-103111.
-
(2006)
Rev. Sci. Instrum.
, vol.77
, pp. 103101-103111
-
-
Tolic-Norrelykke, S.F.1
Schaffer, E.2
Howard, J.3
Pavone, F.S.4
Julicher, F.5
Flyvbjerg, H.6
-
86
-
-
44449136151
-
Recent advances in optical tweezers
-
Moffitt, J.R.; Chemla, Y.R.; Smith, S.B.; Bustamante, C. Recent advances in optical tweezers. Annu. Rev. Biochem. 2008, 77, 205-228.
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 205-228
-
-
Moffitt, J.R.1
Chemla, Y.R.2
Smith, S.B.3
Bustamante, C.4
-
88
-
-
70949101796
-
High-resolution dual-trap optical tweezers with differential detection: An introduction
-
doi:10.1101/pdb.top60
-
Bustamante, C.; Chemla, Y.R.; Moffitt, J.R. High-resolution dual-trap optical tweezers with differential detection: An introduction. Cold Spring Harb. Protoc. 2009, 2009, doi:10.1101/pdb.top60.
-
(2009)
Cold Spring Harb. Protoc. 2009
-
-
Bustamante, C.1
Chemla, Y.R.2
Moffitt, J.R.3
-
89
-
-
28544432440
-
Direct observation of base-pair stepping by RNA polymerase
-
Abbondanzieri, E.A.; Greenleaf, W.J.; Shaevitz, J.W.; Landick, R.; Block, S.M. Direct observation of base-pair stepping by RNA polymerase. Nature 2005, 438, 460-465.
-
(2005)
Nature
, vol.438
, pp. 460-465
-
-
Abbondanzieri, E.A.1
Greenleaf, W.J.2
Shaevitz, J.W.3
Landick, R.4
Block, S.M.5
-
90
-
-
80053144268
-
Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase
-
Cheng, W.; Arunajadai, S.G.; Moffitt, J.R.; Tinoco, I., Jr.; Bustamante, C. Single-base pair unwinding and asynchronous RNA release by the hepatitis C virus NS3 helicase. Science 2011, 333, 1746-1749.
-
(2011)
Science
, vol.333
, pp. 1746-1749
-
-
Cheng, W.1
Arunajadai, S.G.2
Moffitt, J.R.3
Tinoco Jr., I.4
Bustamante, C.5
-
91
-
-
84867090608
-
Ultrafast force-clamp spectroscopy of single molecules reveals load dependence of myosin working stroke
-
Capitanio, M.; Canepari, M.; Maffei, M.; Beneventi, D.; Monico, C.; Vanzi, F.; Bottinelli, R.; Pavone, F.S. Ultrafast force-clamp spectroscopy of single molecules reveals load dependence of myosin working stroke. Nat. Methods 2012, 9, 1013-1019.
-
(2012)
Nat. Methods
, vol.9
, pp. 1013-1019
-
-
Capitanio, M.1
Canepari, M.2
Maffei, M.3
Beneventi, D.4
Monico, C.5
Vanzi, F.6
Bottinelli, R.7
Pavone, F.S.8
-
92
-
-
33847672227
-
Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection
-
Deufel, C.; Forth, S.; Simmons, C.R.; Dejgosha, S.; Wang, M.D. Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection. Nat. Methods 2007, 4, 223-225.
-
(2007)
Nat. Methods
, vol.4
, pp. 223-225
-
-
Deufel, C.1
Forth, S.2
Simmons, C.R.3
Dejgosha, S.4
Wang, M.D.5
-
93
-
-
18144444347
-
Optical torque wrench: Angular trapping, rotation, and torque detection of quartz microparticles
-
La Porta, A.; Wang, M.D. Optical torque wrench: Angular trapping, rotation, and torque detection of quartz microparticles. Phys. Rev. Lett. 2004, 92, 190801.
-
(2004)
Phys. Rev. Lett.
, vol.92
, pp. 190801
-
-
la Porta, A.1
Wang, M.D.2
-
94
-
-
84857315997
-
Calibration of the optical torque wrench
-
Pedaci, F.; Huang, Z.; van Oene, M.; Dekker, N.H. Calibration of the optical torque wrench. Opt. Express 2012, 20, 3787-3802.
-
(2012)
Opt. Express
, vol.20
, pp. 3787-3802
-
-
Pedaci, F.1
Huang, Z.2
van Oene, M.3
Dekker, N.H.4
-
95
-
-
84862615458
-
Recent developments in single-molecule DNA mechanics
-
Bryant, Z.; Oberstrass, F.C.; Basu, A. Recent developments in single-molecule DNA mechanics. Curr. Opin. Struct. Biol. 2012, 22, 304-312.
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 304-312
-
-
Bryant, Z.1
Oberstrass, F.C.2
Basu, A.3
-
96
-
-
20544452797
-
Tracking topoisomerase activity at the single-molecule level
-
Charvin, G.; Strick, T.R.; Bensimon, D.; Croquette, V. Tracking topoisomerase activity at the single-molecule level. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 201-219.
-
(2005)
Annu. Rev. Biophys. Biomol. Struct.
, vol.34
, pp. 201-219
-
-
Charvin, G.1
Strick, T.R.2
Bensimon, D.3
Croquette, V.4
-
97
-
-
77955629227
-
Cellular strategies for regulating DNA supercoiling: A single-molecule perspective
-
Koster, D.A.; Crut, A.; Shuman, S.; Bjornsti, M.A.; Dekker, N.H. Cellular strategies for regulating DNA supercoiling: A single-molecule perspective. Cell 2010, 142, 519-530.
-
(2010)
Cell
, vol.142
, pp. 519-530
-
-
Koster, D.A.1
Crut, A.2
Shuman, S.3
Bjornsti, M.A.4
Dekker, N.H.5
-
98
-
-
1842788676
-
Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation
-
Revyakin, A.; Ebright, R.H.; Strick, T.R. Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation. Proc. Natl. Acad. Sci. USA 2004, 101, 4776-4780.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4776-4780
-
-
Revyakin, A.1
Ebright, R.H.2
Strick, T.R.3
-
99
-
-
84867677392
-
Initiation of transcription-coupled repair characterized at single-molecule resolution
-
Howan, K.; Smith, A.J.; Westblade, L.F.; Joly, N.; Grange, W.; Zorman, S.; Darst, S.A.; Savery, N.J.; Strick, T.R. Initiation of transcription-coupled repair characterized at single-molecule resolution. Nature 2012, 490, 431-434.
-
(2012)
Nature
, vol.490
, pp. 431-434
-
-
Howan, K.1
Smith, A.J.2
Westblade, L.F.3
Joly, N.4
Grange, W.5
Zorman, S.6
Darst, S.A.7
Savery, N.J.8
Strick, T.R.9
-
100
-
-
4344649856
-
Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I
-
Seidel, R.; van Noort, J.; van der Scheer, C.; Bloom, J.G.; Dekker, N.H.; Dutta, C.F.; Blundell, A.; Robinson, T.; Firman, K.; Dekker, C. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat. Struct. Mol. Biol. 2004, 11, 838-843.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 838-843
-
-
Seidel, R.1
van Noort, J.2
van der Scheer, C.3
Bloom, J.G.4
Dekker, N.H.5
Dutta, C.F.6
Blundell, A.7
Robinson, T.8
Firman, K.9
Dekker, C.10
-
101
-
-
43349099320
-
Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping
-
Normanno, D.; Vanzi, F.; Pavone, F.S. Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping. Nucleic Acids Res. 2008, 36, 2505-2513.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 2505-2513
-
-
Normanno, D.1
Vanzi, F.2
Pavone, F.S.3
-
102
-
-
0037169328
-
FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases
-
Aussel, L.; Barre, F.X.; Aroyo, M.; Stasiak, A.; Stasiak, A.Z.; Sherratt, D. FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell 2002, 108, 195-205.
-
(2002)
Cell
, vol.108
, pp. 195-205
-
-
Aussel, L.1
Barre, F.X.2
Aroyo, M.3
Stasiak, A.4
Stasiak, A.Z.5
Sherratt, D.6
-
103
-
-
20444500568
-
Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking
-
Saleh, O.A.; Bigot, S.; Barre, F.X.; Allemand, J.F. Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking. Nat. Struct. Mol. Biol. 2005, 12, 436-440.
-
(2005)
Nat. Struct. Mol. Biol.
, vol.12
, pp. 436-440
-
-
Saleh, O.A.1
Bigot, S.2
Barre, F.X.3
Allemand, J.F.4
-
104
-
-
0023433855
-
Supercoiling of the DNA template during transcription
-
Liu, L.F.; Wang, J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 1987, 84, 7024-7027.
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 7024-7027
-
-
Liu, L.F.1
Wang, J.C.2
-
105
-
-
0000559443
-
Three-dimensional magneto-optic trap for micro-object manipulation
-
Sacconi, L.; Romano, G.; Ballerini, R.; Capitanio, M.; De Pas, M.; Giuntini, M.; Dunlap, D.; Finzi, L.; Pavone, F.S. Three-dimensional magneto-optic trap for micro-object manipulation. Opt. Lett. 2001, 26, 1359-1361.
-
(2001)
Opt. Lett.
, vol.26
, pp. 1359-1361
-
-
Sacconi, L.1
Romano, G.2
Ballerini, R.3
Capitanio, M.4
de Pas, M.5
Giuntini, M.6
Dunlap, D.7
Finzi, L.8
Pavone, F.S.9
-
106
-
-
0037438725
-
Force and torque measurements using magnetic micro beads for single molecule biophysics
-
Romano, G.; Sacconi, L.; Capitanio, M.; Pavone, F.S. Force and torque measurements using magnetic micro beads for single molecule biophysics. Opt. Commun. 2003, 215, 323-331.
-
(2003)
Opt. Commun.
, vol.215
, pp. 323-331
-
-
Romano, G.1
Sacconi, L.2
Capitanio, M.3
Pavone, F.S.4
-
107
-
-
42749099817
-
Spin absorption, windmill, and magneto-optic effects in optical angular momentum transfer
-
Normanno, D.; Capitanio, M.; Pavone, F.S. Spin absorption, windmill, and magneto-optic effects in optical angular momentum transfer. Phys. Rev. A 2004, 70, 053829.
-
(2004)
Phys. Rev. A
, vol.70
, pp. 053829
-
-
Normanno, D.1
Capitanio, M.2
Pavone, F.S.3
-
108
-
-
6444239874
-
High-precision measurements of light-induced torque on absorbing microspheres
-
Capitanio, M.; Normanno, D.; Pavone, F.S. High-precision measurements of light-induced torque on absorbing microspheres. Opt. Lett. 2004, 29, 2231-2233.
-
(2004)
Opt. Lett.
, vol.29
, pp. 2231-2233
-
-
Capitanio, M.1
Normanno, D.2
Pavone, F.S.3
-
109
-
-
78649709362
-
Magnetic torque tweezers: Measuring torsional stiffness in DNA and RecA-DNA filaments
-
Lipfert, J.; Kerssemakers, J.W.; Jager, T.; Dekker, N.H. Magnetic torque tweezers: Measuring torsional stiffness in DNA and RecA-DNA filaments. Nat. Methods 2010, 7, 977-980.
-
(2010)
Nat. Methods
, vol.7
, pp. 977-980
-
-
Lipfert, J.1
Kerssemakers, J.W.2
Jager, T.3
Dekker, N.H.4
-
110
-
-
65249161305
-
Magnetic tweezers measurement of single molecule torque
-
Celedon, A.; Nodelman, I.M.; Wildt, B.; Dewan, R.; Searson, P.; Wirtz, D.; Bowman, G.D.; Sun, S.X. Magnetic tweezers measurement of single molecule torque. Nano Lett. 2009, 9, 1720-1725.
-
(2009)
Nano Lett.
, vol.9
, pp. 1720-1725
-
-
Celedon, A.1
Nodelman, I.M.2
Wildt, B.3
Dewan, R.4
Searson, P.5
Wirtz, D.6
Bowman, G.D.7
Sun, S.X.8
-
111
-
-
66149144002
-
Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber
-
Kruithof, M.; Chien, F.T.; Routh, A.; Logie, C.; Rhodes, D.; van Noort, J. Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber. Nat. Struct. Mol. Biol. 2009, 16, 534-540.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 534-540
-
-
Kruithof, M.1
Chien, F.T.2
Routh, A.3
Logie, C.4
Rhodes, D.5
van Noort, J.6
-
112
-
-
84861401482
-
Recent advances in magnetic tweezers
-
De Vlaminck, I.; Dekker, C. Recent advances in magnetic tweezers. Annu. Rev. Biophys. 2012, 41, 453-472.
-
(2012)
Annu. Rev. Biophys.
, vol.41
, pp. 453-472
-
-
de Vlaminck, I.1
Dekker, C.2
-
113
-
-
0036111913
-
Magnetic tweezers: Micromanipulation and force measurement at the molecular level
-
Gosse, C.; Croquette, V. Magnetic tweezers: Micromanipulation and force measurement at the molecular level. Biophys. J. 2002, 82, 3314-3329.
-
(2002)
Biophys. J.
, vol.82
, pp. 3314-3329
-
-
Gosse, C.1
Croquette, V.2
-
114
-
-
80054730808
-
Magnetic tweezers for single-molecule manipulation
-
Seol, Y.; Neuman, K.C. Magnetic tweezers for single-molecule manipulation. Methods Mol. Biol. 2011, 783, 265-293.
-
(2011)
Methods Mol. Biol.
, vol.783
, pp. 265-293
-
-
Seol, Y.1
Neuman, K.C.2
-
115
-
-
0028032302
-
Alignment and sensitive detection of DNA by a moving interface
-
Bensimon, A.; Simon, A.; Chiffaudel, A.; Croquette, V.; Heslot, F.; Bensimon, D. Alignment and sensitive detection of DNA by a moving interface. Science 1994, 265, 2096-2098.
-
(1994)
Science
, vol.265
, pp. 2096-2098
-
-
Bensimon, A.1
Simon, A.2
Chiffaudel, A.3
Croquette, V.4
Heslot, F.5
Bensimon, D.6
-
116
-
-
34547138714
-
Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules
-
Kim, J.H.; Larson, R.G. Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules. Nucleic Acids Res. 2007, 35, 3848-3858.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 3848-3858
-
-
Kim, J.H.1
Larson, R.G.2
-
117
-
-
3242886361
-
Single DNA molecule analysis: Applications of molecular combing
-
Lebofsky, R.; Bensimon, A. Single DNA molecule analysis: Applications of molecular combing. Briefings Funct. Genomics Proteomics 2003, 1, 385-396.
-
(2003)
Briefings Funct. Genomics Proteomics
, vol.1
, pp. 385-396
-
-
Lebofsky, R.1
Bensimon, A.2
-
118
-
-
52649162907
-
DNA curtains and nanoscale curtain rods: High-throughput tools for single molecule imaging
-
Fazio, T.; Visnapuu, M.L.; Wind, S.; Greene, E.C. DNA curtains and nanoscale curtain rods: High-throughput tools for single molecule imaging. Langmuir 2008, 24, 10524-10531.
-
(2008)
Langmuir
, vol.24
, pp. 10524-10531
-
-
Fazio, T.1
Visnapuu, M.L.2
Wind, S.3
Greene, E.C.4
-
119
-
-
22244490690
-
Single-molecule studies of repressor-DNA interactions show long-range interactions
-
Wang, Y.M.; Tegenfeldt, J.O.; Reisner, W.; Riehn, R.; Guan, X.J.; Guo, L.; Golding, I.; Cox, E.C.; Sturm, J.; Austin, R.H. Single-molecule studies of repressor-DNA interactions show long-range interactions. Proc. Natl. Acad. Sci. USA 2005, 102, 9796-9801.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 9796-9801
-
-
Wang, Y.M.1
Tegenfeldt, J.O.2
Reisner, W.3
Riehn, R.4
Guan, X.J.5
Guo, L.6
Golding, I.7
Cox, E.C.8
Sturm, J.9
Austin, R.H.10
-
120
-
-
34249932435
-
Probing transcription factor dynamics at the single-molecule level in a living cell
-
Elf, J.; Li, G.W.; Xie, X.S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 2007, 316, 1191-1194.
-
(2007)
Science
, vol.316
, pp. 1191-1194
-
-
Elf, J.1
Li, G.W.2
Xie, X.S.3
-
121
-
-
0027749617
-
Visualization of single molecules of RNA polymerase sliding along DNA
-
Kabata, H.; Kurosawa, O.; Arai, I.; Washizu, M.; Margarson, S.A.; Glass, R.E.; Shimamoto, N. Visualization of single molecules of RNA polymerase sliding along DNA. Science 1993, 262, 1561-1563.
-
(1993)
Science
, vol.262
, pp. 1561-1563
-
-
Kabata, H.1
Kurosawa, O.2
Arai, I.3
Washizu, M.4
Margarson, S.A.5
Glass, R.E.6
Shimamoto, N.7
-
122
-
-
33645807371
-
A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
-
Blainey, P.C.; van Oijen, A.M.; Banerjee, A.; Verdine, G.L.; Xie, X.S. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl. Acad. Sci. USA 2006, 103, 5752-5757.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 5752-5757
-
-
Blainey, P.C.1
van Oijen, A.M.2
Banerjee, A.3
Verdine, G.L.4
Xie, X.S.5
-
123
-
-
35649018595
-
Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6
-
Gorman, J.; Chowdhury, A.; Surtees, J.A.; Shimada, J.; Reichman, D.R.; Alani, E.; Greene, E.C. Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell 2007, 28, 359-370.
-
(2007)
Mol. Cell
, vol.28
, pp. 359-370
-
-
Gorman, J.1
Chowdhury, A.2
Surtees, J.A.3
Shimada, J.4
Reichman, D.R.5
Alani, E.6
Greene, E.C.7
-
124
-
-
46749108829
-
Tumor suppressor p53 slides on DNA with low friction and high stability
-
Tafvizi, A.; Huang, F.; Leith, J.S.; Fersht, A.R.; Mirny, L.A.; van Oijen, A.M. Tumor suppressor p53 slides on DNA with low friction and high stability. Biophys. J. 2008, 95, L01-L03.
-
(2008)
Biophys. J.
, vol.95
-
-
Tafvizi, A.1
Huang, F.2
Leith, J.S.3
Fersht, A.R.4
Mirny, L.A.5
van Oijen, A.M.6
-
125
-
-
79952259642
-
A single-molecule characterization of p53 search on DNA
-
Tafvizi, A.; Huang, F.; Fersht, A.R.; Mirny, L.A.; van Oijen, A.M. A single-molecule characterization of p53 search on DNA. Proc. Natl. Acad. Sci. USA 2011, 108, 563-568.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 563-568
-
-
Tafvizi, A.1
Huang, F.2
Fersht, A.R.3
Mirny, L.A.4
van Oijen, A.M.5
-
126
-
-
31944435731
-
Long-distance lateral diffusion of human Rad51 on double-stranded DNA
-
Graneli, A.; Yeykal, C.C.; Robertson, R.B.; Greene, E.C. Long-distance lateral diffusion of human Rad51 on double-stranded DNA. Proc. Natl. Acad. Sci. USA 2006, 103, 1221-1226.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 1221-1226
-
-
Graneli, A.1
Yeykal, C.C.2
Robertson, R.B.3
Greene, E.C.4
-
127
-
-
47249153641
-
Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA
-
Bonnet, I.; Biebricher, A.; Porte, P.L.; Loverdo, C.; Benichou, O.; Voituriez, R.; Escude, C.; Wende, W.; Pingoud, A.; Desbiolles, P. Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA. Nucleic Acids Res. 2008, 36, 4118-4127.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 4118-4127
-
-
Bonnet, I.1
Biebricher, A.2
Porte, P.L.3
Loverdo, C.4
Benichou, O.5
Voituriez, R.6
Escude, C.7
Wende, W.8
Pingoud, A.9
Desbiolles, P.10
-
128
-
-
0018472170
-
The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations
-
Schurr, J.M. The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations. Biophys. Chem. 1979, 9, 413-414.
-
(1979)
Biophys. Chem.
, vol.9
, pp. 413-414
-
-
Schurr, J.M.1
-
129
-
-
71449094444
-
Nonspecifically bound proteins spin while diffusing along DNA
-
Blainey, P.C.; Luo, G.; Kou, S.C.; Mangel, W.F.; Verdine, G.L.; Bagchi, B.; Xie, X.S. Nonspecifically bound proteins spin while diffusing along DNA. Nat. Struct. Mol. Biol. 2009, 16, 1224-1229.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1224-1229
-
-
Blainey, P.C.1
Luo, G.2
Kou, S.C.3
Mangel, W.F.4
Verdine, G.L.5
Bagchi, B.6
Xie, X.S.7
-
130
-
-
79952494759
-
Protein sliding and hopping kinetics on DNA
-
DeSantis, M.C.; Li, J.L.; Wang, Y.M. Protein sliding and hopping kinetics on DNA. Phys. Rev. E 2011, 83, 021907.
-
(2011)
Phys. Rev. E
, vol.83
, pp. 021907
-
-
DeSantis, M.C.1
Li, J.L.2
Wang, Y.M.3
-
131
-
-
65549138947
-
Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins
-
Loverdo, C.; Benichou, O.; Voituriez, R.; Biebricher, A.; Bonnet, I.; Desbiolles, P. Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins. Phys. Rev. Lett. 2009, 102, 188101.
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 188101
-
-
Loverdo, C.1
Benichou, O.2
Voituriez, R.3
Biebricher, A.4
Bonnet, I.5
Desbiolles, P.6
-
132
-
-
84861382411
-
The rotation-coupled sliding of EcoRV
-
Dikic, J.; Menges, C.; Clarke, S.; Kokkinidis, M.; Pingoud, A.; Wende, W.; Desbiolles, P. The rotation-coupled sliding of EcoRV. Nucleic Acids Res. 2012, 40, 4064-4070.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 4064-4070
-
-
Dikic, J.1
Menges, C.2
Clarke, S.3
Kokkinidis, M.4
Pingoud, A.5
Wende, W.6
Desbiolles, P.7
-
133
-
-
77955416347
-
Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice
-
Gorman, J.; Plys, A.J.; Visnapuu, M.L.; Alani, E.; Greene, E.C. Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice. Nat. Struct. Mol. Biol. 2010, 17, 932-938.
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 932-938
-
-
Gorman, J.1
Plys, A.J.2
Visnapuu, M.L.3
Alani, E.4
Greene, E.C.5
-
134
-
-
78650307167
-
Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase
-
Finkelstein, I.J.; Visnapuu, M.L.; Greene, E.C. Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase. Nature 2010, 468, 983-987.
-
(2010)
Nature
, vol.468
, pp. 983-987
-
-
Finkelstein, I.J.1
Visnapuu, M.L.2
Greene, E.C.3
-
135
-
-
77957023630
-
Watching individual proteins acting on single molecules of DNA
-
Amitani, I.; Liu, B.A.; Dombrowski, C.C.; Baskin, R.J.; Kowalczykowski, S.C. Watching individual proteins acting on single molecules of DNA. Methods Enzymol. 2010, 472, 261-291.
-
(2010)
Methods Enzymol.
, vol.472
, pp. 261-291
-
-
Amitani, I.1
Liu, B.A.2
Dombrowski, C.C.3
Baskin, R.J.4
Kowalczykowski, S.C.5
-
136
-
-
0035905687
-
Processive translocation and DNA unwinding by individual RecBCD enzyme molecules
-
Bianco, P.R.; Brewer, L.R.; Corzett, M.; Balhorn, R.; Yeh, Y.; Kowalczykowski, S.C.; Baskin, R.J. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 2001, 409, 374-378.
-
(2001)
Nature
, vol.409
, pp. 374-378
-
-
Bianco, P.R.1
Brewer, L.R.2
Corzett, M.3
Balhorn, R.4
Yeh, Y.5
Kowalczykowski, S.C.6
Baskin, R.J.7
-
137
-
-
0141540814
-
A molecular throttle: The recombination hotspot chi controls DNA translocation by the RecBCD helicase
-
Spies, M.; Bianco, P.R.; Dillingham, M.S.; Handa, N.; Baskin, R.J.; Kowalczykowski, S.C. A molecular throttle: The recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell 2003, 114, 647-654.
-
(2003)
Cell
, vol.114
, pp. 647-654
-
-
Spies, M.1
Bianco, P.R.2
Dillingham, M.S.3
Handa, N.4
Baskin, R.J.5
Kowalczykowski, S.C.6
-
138
-
-
36049052525
-
RecBCD enzyme switches lead motor subunits in response to chi recognition
-
Spies, M.; Amitani, I.; Baskin, R.J.; Kowalczykowski, S.C. RecBCD enzyme switches lead motor subunits in response to chi recognition. Cell 2007, 131, 694-705.
-
(2007)
Cell
, vol.131
, pp. 694-705
-
-
Spies, M.1
Amitani, I.2
Baskin, R.J.3
Kowalczykowski, S.C.4
-
139
-
-
48349090299
-
See me, feel me: Methods to concurrently visualize and manipulate single DNA molecules and associated proteins
-
Van Mameren, J.; Peterman, E.J.; Wuite, G.J. See me, feel me: Methods to concurrently visualize and manipulate single DNA molecules and associated proteins. Nucleic Acids Res. 2008, 36, 4381-4389.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 4381-4389
-
-
van Mameren, J.1
Peterman, E.J.2
Wuite, G.J.3
-
140
-
-
34247627435
-
Stretching and immobilization of DNA for studies of protein-DNA interactions at the single-molecule level
-
Kim, J.H.; Dukkipati, V.R.; Pang, S.W.; Larson, R.G. Stretching and immobilization of DNA for studies of protein-DNA interactions at the single-molecule level. Nanoscale Res. Lett. 2007, 2, 185-201.
-
(2007)
Nanoscale Res. Lett.
, vol.2
, pp. 185-201
-
-
Kim, J.H.1
Dukkipati, V.R.2
Pang, S.W.3
Larson, R.G.4
-
141
-
-
33745162550
-
Differential detection of dual traps improves the spatial resolution of optical tweezers
-
Moffitt, J.R.; Chemla, Y.R.; Izhaky, D.; Bustamante, C. Differential detection of dual traps improves the spatial resolution of optical tweezers. Proc. Natl. Acad. Sci. USA 2006, 103, 9006-9011.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 9006-9011
-
-
Moffitt, J.R.1
Chemla, Y.R.2
Izhaky, D.3
Bustamante, C.4
-
142
-
-
0346258014
-
Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
-
Shaevitz, J.W.; Abbondanzieri, E.A.; Landick, R.; Block, S.M. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 2003, 426, 684-687.
-
(2003)
Nature
, vol.426
, pp. 684-687
-
-
Shaevitz, J.W.1
Abbondanzieri, E.A.2
Landick, R.3
Block, S.M.4
-
143
-
-
0033869089
-
An integrated laser trap/flow control video microscope for the study of single biomolecules
-
Wuite, G.J.L.; Davenport, R.J.; Rappaport, A.; Bustamante, C. An integrated laser trap/flow control video microscope for the study of single biomolecules. Biophys. J. 2000, 79, 1155-1167.
-
(2000)
Biophys. J.
, vol.79
, pp. 1155-1167
-
-
Wuite, G.J.L.1
Davenport, R.J.2
Rappaport, A.3
Bustamante, C.4
-
144
-
-
84861442263
-
Active DNA unwinding dynamics during processive DNA replication
-
Morin, J.A.; Cao, F.J.; Lazaro, J.M.; Arias-Gonzalez, J.R.; Valpuesta, J.M.; Carrascosa, J.L.; Salas, M.; Ibarra, B. Active DNA unwinding dynamics during processive DNA replication. Proc. Natl. Acad. Sci. USA 2012, 109, 8115-8120.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 8115-8120
-
-
Morin, J.A.1
Cao, F.J.2
Lazaro, J.M.3
Arias-Gonzalez, J.R.4
Valpuesta, J.M.5
Carrascosa, J.L.6
Salas, M.7
Ibarra, B.8
-
145
-
-
24144478521
-
Mechanism of force generation of a viral DNA packaging motor
-
Chemla, Y.R.; Aathavan, K.; Michaelis, J.; Grimes, S.; Jardine, P.J.; Anderson, D.L.; Bustamante, C. Mechanism of force generation of a viral DNA packaging motor. Cell 2005, 122, 683-692.
-
(2005)
Cell
, vol.122
, pp. 683-692
-
-
Chemla, Y.R.1
Aathavan, K.2
Michaelis, J.3
Grimes, S.4
Jardine, P.J.5
Anderson, D.L.6
Bustamante, C.7
-
146
-
-
58749087869
-
Intersubunit coordination in a homomeric ring ATPase
-
Moffitt, J.R.; Chemla, Y.R.; Aathavan, K.; Grimes, S.; Jardine, P.J.; Anderson, D.L.; Bustamante, C. Intersubunit coordination in a homomeric ring ATPase. Nature 2009, 457, 446-450.
-
(2009)
Nature
, vol.457
, pp. 446-450
-
-
Moffitt, J.R.1
Chemla, Y.R.2
Aathavan, K.3
Grimes, S.4
Jardine, P.J.5
Anderson, D.L.6
Bustamante, C.7
-
147
-
-
0035909370
-
The bacteriophage straight phi29 portal motor can package DNA against a large internal force
-
Smith, D.E.; Tans, S.J.; Smith, S.B.; Grimes, S.; Anderson, D.L.; Bustamante, C. The bacteriophage straight phi29 portal motor can package DNA against a large internal force. Nature 2001, 413, 748-752.
-
(2001)
Nature
, vol.413
, pp. 748-752
-
-
Smith, D.E.1
Tans, S.J.2
Smith, S.B.3
Grimes, S.4
Anderson, D.L.5
Bustamante, C.6
-
148
-
-
77953811389
-
Mechanochemistry of a viral DNA packaging motor
-
Yu, J.; Moffitt, J.; Hetherington, C.L.; Bustamante, C.; Oster, G. Mechanochemistry of a viral DNA packaging motor. J. Mol. Biol. 2010, 400, 186-203.
-
(2010)
J. Mol. Biol.
, vol.400
, pp. 186-203
-
-
Yu, J.1
Moffitt, J.2
Hetherington, C.L.3
Bustamante, C.4
Oster, G.5
-
149
-
-
0034958378
-
Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers
-
Bennink, M.L.; Leuba, S.H.; Leno, G.H.; Zlatanova, J.; de Grooth, B.G.; Greve, J. Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers. Nat. Struct. Biol. 2001, 8, 606-610.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 606-610
-
-
Bennink, M.L.1
Leuba, S.H.2
Leno, G.H.3
Zlatanova, J.4
de Grooth, B.G.5
Greve, J.6
-
150
-
-
0034602688
-
Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure
-
Cui, Y.; Bustamante, C. Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc. Natl. Acad. Sci. USA 2000, 97, 127-132.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 127-132
-
-
Cui, Y.1
Bustamante, C.2
-
151
-
-
68149120313
-
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
-
Hodges, C.; Bintu, L.; Lubkowska, L.; Kashlev, M.; Bustamante, C. Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 2009, 325, 626-628.
-
(2009)
Science
, vol.325
, pp. 626-628
-
-
Hodges, C.1
Bintu, L.2
Lubkowska, L.3
Kashlev, M.4
Bustamante, C.5
-
152
-
-
19444384194
-
DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway
-
Van den Broek, B.; Noom, M.C.; Wuite, G.J.L. DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway. Nucleic Acids Res. 2005, 33, 2676-2684.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2676-2684
-
-
Van den Broek, B.1
Noom, M.C.2
Wuite, G.J.L.3
-
153
-
-
57349153045
-
How DNA coiling enhances target localization by proteins
-
Van den Broek, B.; Lomholt, M.A.; Kalisch, S.M.J.; Metzler, R.; Wuite, G.J.L. How DNA coiling enhances target localization by proteins. Proc. Natl. Acad. Sci. USA 2008, 105, 15738-15742.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 15738-15742
-
-
Van den Broek, B.1
Lomholt, M.A.2
Kalisch, S.M.J.3
Metzler, R.4
Wuite, G.J.L.5
-
154
-
-
79953873168
-
Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA-protein interactions
-
Candelli, A.; Wuite, G.J.; Peterman, E.J. Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA-protein interactions. Phys. Chem. Chem. Phys. 2011, 13, 7263-7272.
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 7263-7272
-
-
Candelli, A.1
Wuite, G.J.2
Peterman, E.J.3
-
155
-
-
34548669597
-
FIONA in the trap: The advantages of combining optical tweezers and fluorescence
-
Capitanio, M.; Maggi, D.; Vanzi, F.; Pavone, F.S. FIONA in the trap: The advantages of combining optical tweezers and fluorescence. J. Opt. A 2007, 9, S157-S163.
-
(2007)
J. Opt. A
, vol.9
-
-
Capitanio, M.1
Maggi, D.2
Vanzi, F.3
Pavone, F.S.4
-
156
-
-
0033021362
-
Single-molecule imaging of RNA polymerase-DNA interactions in real time
-
Harada, Y.; Funatsu, T.; Murakami, K.; Nonoyama, Y.; Ishihama, A.; Yanagida, T. Single-molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 1999, 76, 709-715.
-
(1999)
Biophys. J.
, vol.76
, pp. 709-715
-
-
Harada, Y.1
Funatsu, T.2
Murakami, K.3
Nonoyama, Y.4
Ishihama, A.5
Yanagida, T.6
-
157
-
-
59649116344
-
Counting RAD51 proteins disassembling from nucleoprotein filaments under tension
-
Van Mameren, J.; Modesti, M.; Kanaar, R.; Wyman, C.; Peterman, E.J.G.; Wuite, G.J.L. Counting RAD51 proteins disassembling from nucleoprotein filaments under tension. Nature 2009, 457, 745-748.
-
(2009)
Nature
, vol.457
, pp. 745-748
-
-
van Mameren, J.1
Modesti, M.2
Kanaar, R.3
Wyman, C.4
Peterman, E.J.G.5
Wuite, G.J.L.6
-
158
-
-
67649394764
-
Tracking of single quantum dot labeled EcoRV sliding along DNA manipulated by double optical tweezers
-
Biebricher, A.; Wende, W.; Escude, C.; Pingoud, A.; Desbiolles, P. Tracking of single quantum dot labeled EcoRV sliding along DNA manipulated by double optical tweezers. Biophys. J. 2009, 96, L50-L52.
-
(2009)
Biophys. J.
, vol.96
-
-
Biebricher, A.1
Wende, W.2
Escude, C.3
Pingoud, A.4
Desbiolles, P.5
-
159
-
-
50849104529
-
Quantum dots versus organic dyes as fluorescent labels
-
Resch-Genger, U.; Grabolle, M.; Cavaliere-Jaricot, S.; Nitschke, R.; Nann, T. Quantum dots versus organic dyes as fluorescent labels. Nat. Methods 2008, 5, 763-775.
-
(2008)
Nat. Methods
, vol.5
, pp. 763-775
-
-
Resch-Genger, U.1
Grabolle, M.2
Cavaliere-Jaricot, S.3
Nitschke, R.4
Nann, T.5
-
160
-
-
2642522184
-
Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores
-
Dijk, M.A.; Kapitein, L.C.; Mameren, J.; Schmidt, C.F.; Peterman, E.J. Combining optical trapping and single-molecule fluorescence spectroscopy: Enhanced photobleaching of fluorophores. J. Phys. Chem. B 2004, 108, 6479-6484.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6479-6484
-
-
Dijk, M.A.1
Kapitein, L.C.2
Mameren, J.3
Schmidt, C.F.4
Peterman, E.J.5
-
161
-
-
77954586689
-
Combining optical tweezers, single-molecule fluorescence microscopy, and microfluidics for studies of DNA-protein interactions
-
Gross, P.; Farge, G.; Peterman, E.J.; Wuite, G.J. Combining optical tweezers, single-molecule fluorescence microscopy, and microfluidics for studies of DNA-protein interactions. Methods Enzymol. 2010, 475, 427-453.
-
(2010)
Methods Enzymol.
, vol.475
, pp. 427-453
-
-
Gross, P.1
Farge, G.2
Peterman, E.J.3
Wuite, G.J.4
-
162
-
-
33746702015
-
Interlaced optical force-fluorescence measurements for single molecule biophysics
-
Brau, R.R.; Tarsa, P.B.; Ferrer, J.M.; Lee, P.; Lang, M.J. Interlaced optical force-fluorescence measurements for single molecule biophysics. Biophys. J. 2006, 91, 1069-1077.
-
(2006)
Biophys. J.
, vol.91
, pp. 1069-1077
-
-
Brau, R.R.1
Tarsa, P.B.2
Ferrer, J.M.3
Lee, P.4
Lang, M.J.5
-
163
-
-
79953292607
-
Ultrahigh-resolution optical trap with single-fluorophore sensitivity
-
Comstock, M.J.; Ha, T.; Chemla, Y.R. Ultrahigh-resolution optical trap with single-fluorophore sensitivity. Nat. Methods 2011, 8, 335-340.
-
(2011)
Nat. Methods
, vol.8
, pp. 335-340
-
-
Comstock, M.J.1
Ha, T.2
Chemla, Y.R.3
-
164
-
-
77954608777
-
Super-accuracy and super-resolution getting around the diffraction limit
-
Toprak, E.; Kural, C.; Selvin, P.R. Super-accuracy and super-resolution getting around the diffraction limit. Methods Enzymol. 2010, 475, 1-26.
-
(2010)
Methods Enzymol.
, vol.475
, pp. 1-26
-
-
Toprak, E.1
Kural, C.2
Selvin, P.R.3
-
165
-
-
80054723783
-
Fluorescence imaging with one nanometer accuracy: In vitro and in vivo studies of molecular motors
-
Hoffman, M.T.; Sheung, J.; Selvin, P.R. Fluorescence imaging with one nanometer accuracy: In vitro and in vivo studies of molecular motors. Methods Mol. Biol. 2011, 778, 33-56.
-
(2011)
Methods Mol. Biol.
, vol.778
, pp. 33-56
-
-
Hoffman, M.T.1
Sheung, J.2
Selvin, P.R.3
-
166
-
-
44449097780
-
Do-it-yourself guide: How to use the modern single-molecule toolkit
-
Walter, N.G.; Huang, C.Y.; Manzo, A.J.; Sobhy, M.A. Do-it-yourself guide: How to use the modern single-molecule toolkit. Nat. Methods 2008, 5, 475-489.
-
(2008)
Nat. Methods
, vol.5
, pp. 475-489
-
-
Walter, N.G.1
Huang, C.Y.2
Manzo, A.J.3
Sobhy, M.A.4
-
167
-
-
80054721875
-
A brief introduction to single-molecule fluorescence methods
-
Van den Wildenberg, S.M.; Prevo, B.; Peterman, E.J. A brief introduction to single-molecule fluorescence methods. Methods Mol. Biol. 2011, 783, 81-99.
-
(2011)
Methods Mol. Biol.
, vol.783
, pp. 81-99
-
-
Van den Wildenberg, S.M.1
Prevo, B.2
Peterman, E.J.3
-
168
-
-
0036231415
-
Precise nanometer localization analysis for individual fluorescent probes
-
Thompson, R.E.; Larson, D.R.; Webb, W.W. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 2002, 82, 2775-2783.
-
(2002)
Biophys. J.
, vol.82
, pp. 2775-2783
-
-
Thompson, R.E.1
Larson, D.R.2
Webb, W.W.3
-
169
-
-
0037832404
-
Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization
-
Yildiz, A.; Forkey, J.N.; McKinney, S.A.; Ha, T.; Goldman, Y.E.; Selvin, P.R. Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization. Science 2003, 300, 2061-2065.
-
(2003)
Science
, vol.300
, pp. 2061-2065
-
-
Yildiz, A.1
Forkey, J.N.2
McKinney, S.A.3
Ha, T.4
Goldman, Y.E.5
Selvin, P.R.6
-
170
-
-
79953725152
-
Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA
-
Graham, J.S.; Johnson, R.C.; Marko, J.F. Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res. 2011, 39, 2249-2259.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 2249-2259
-
-
Graham, J.S.1
Johnson, R.C.2
Marko, J.F.3
-
171
-
-
63849284078
-
Effects of macromolecular crowding and DNA looping on gene regulation kinetics
-
Li, G.W.; Berg, O.G.; Elf, J. Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nat. Phys. 2009, 5, 294-297.
-
(2009)
Nat. Phys.
, vol.5
, pp. 294-297
-
-
Li, G.W.1
Berg, O.G.2
Elf, J.3
-
172
-
-
0017192686
-
Mobility measurement by analysis of fluorescence photobleaching recovery kinetics
-
Axelrod, D.; Koppel, D.E.; Schlessinger, J.; Elson, E.; Webb, W.W. Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Biophys. J. 1976, 16, 1055-1069.
-
(1976)
Biophys. J.
, vol.16
, pp. 1055-1069
-
-
Axelrod, D.1
Koppel, D.E.2
Schlessinger, J.3
Elson, E.4
Webb, W.W.5
-
173
-
-
33645969033
-
Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins
-
Beaudouin, J.; Mora-Bermudez, F.; Klee, T.; Daigle, N.; Ellenberg, J. Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins. Biophys. J. 2006, 90, 1878-1894.
-
(2006)
Biophys. J.
, vol.90
, pp. 1878-1894
-
-
Beaudouin, J.1
Mora-Bermudez, F.2
Klee, T.3
Daigle, N.4
Ellenberg, J.5
-
174
-
-
33746805521
-
Analysis of binding at a single spatially localized cluster of binding sites by fluorescence recovery after photobleaching
-
Sprague, B.L.; Muller, F.; Pego, R.L.; Bungay, P.M.; Stavreva, D.A.; McNally, J.G. Analysis of binding at a single spatially localized cluster of binding sites by fluorescence recovery after photobleaching. Biophys. J. 2006, 91, 1169-1191.
-
(2006)
Biophys. J.
, vol.91
, pp. 1169-1191
-
-
Sprague, B.L.1
Muller, F.2
Pego, R.L.3
Bungay, P.M.4
Stavreva, D.A.5
McNally, J.G.6
-
175
-
-
3042760021
-
Global nature of dynamic protein-chromatin interactions in vivo: Three-dimensional genome scanning and dynamic interaction networks of chromatin proteins
-
Phair, R.D.; Scaffidi, P.; Elbi, C.; Vecerova, J.; Dey, A.; Ozato, K.; Brown, D.T.; Hager, G.; Bustin, M.; Misteli, T. Global nature of dynamic protein-chromatin interactions in vivo: Three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol. Cell. Biol. 2004, 24, 6393-6402.
-
(2004)
Mol. Cell. Biol.
, vol.24
, pp. 6393-6402
-
-
Phair, R.D.1
Scaffidi, P.2
Elbi, C.3
Vecerova, J.4
Dey, A.5
Ozato, K.6
Brown, D.T.7
Hager, G.8
Bustin, M.9
Misteli, T.10
-
176
-
-
13244291467
-
FRAP analysis of binding: Proper and fitting
-
Sprague, B.L.; McNally, J.G. FRAP analysis of binding: Proper and fitting. Trends Cell Biol. 2005, 15, 84-91.
-
(2005)
Trends Cell Biol.
, vol.15
, pp. 84-91
-
-
Sprague, B.L.1
McNally, J.G.2
-
177
-
-
43149119497
-
Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching
-
Mueller, F.; Wach, P.; McNally, J.G. Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching. Biophys. J. 2008, 94, 3323-3339.
-
(2008)
Biophys. J.
, vol.94
, pp. 3323-3339
-
-
Mueller, F.1
Wach, P.2
McNally, J.G.3
-
178
-
-
2242433534
-
A kinetic framework for a mammalian RNA polymerase in vivo
-
Dundr, M.; Hoffmann-Rohrer, U.; Hu, Q.; Grummt, I.; Rothblum, L.I.; Phair, R.D.; Misteli, T. A kinetic framework for a mammalian RNA polymerase in vivo. Science 2002, 298, 1623-1626.
-
(2002)
Science
, vol.298
, pp. 1623-1626
-
-
Dundr, M.1
Hoffmann-Rohrer, U.2
Hu, Q.3
Grummt, I.4
Rothblum, L.I.5
Phair, R.D.6
Misteli, T.7
-
179
-
-
0037049641
-
The transcription cycle of RNA polymerase II in living cells
-
Kimura, H.; Sugaya, K.; Cook, P.R. The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 2002, 159, 777-782.
-
(2002)
J. Cell Biol.
, vol.159
, pp. 777-782
-
-
Kimura, H.1
Sugaya, K.2
Cook, P.R.3
-
180
-
-
34548507690
-
In vivo dynamics of RNA polymerase II transcription
-
Darzacq, X.; Shav-Tal, Y.; de Turris, V.; Brody, Y.; Shenoy, S.M.; Phair, R.D.; Singer, R.H. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 2007, 14, 796-806.
-
(2007)
Nat. Struct. Mol. Biol.
, vol.14
, pp. 796-806
-
-
Darzacq, X.1
Shav-Tal, Y.2
de Turris, V.3
Brody, Y.4
Shenoy, S.M.5
Phair, R.D.6
Singer, R.H.7
-
181
-
-
60349125976
-
Fluorescence recovery after photobleaching (FRAP) to study nuclear protein dynamics in living cells
-
Van Royen, M.E.; Farla, P.; Mattern, K.A.; Geverts, B.; Trapman, J.; Houtsmuller, A.B. Fluorescence recovery after photobleaching (FRAP) to study nuclear protein dynamics in living cells. Methods Mol. Biol. 2009, 464, 363-385.
-
(2009)
Methods Mol. Biol.
, vol.464
, pp. 363-385
-
-
van Royen, M.E.1
Farla, P.2
Mattern, K.A.3
Geverts, B.4
Trapman, J.5
Houtsmuller, A.B.6
-
182
-
-
0032828419
-
Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one-and two-photon excitation
-
Schwille, P.; Haupts, U.; Maiti, S.; Webb, W.W. Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one-and two-photon excitation. Biophys. J. 1999, 77, 2251-2265.
-
(1999)
Biophys. J.
, vol.77
, pp. 2251-2265
-
-
Schwille, P.1
Haupts, U.2
Maiti, S.3
Webb, W.W.4
-
183
-
-
0034755570
-
Fluorescence correlation spectroscopy measures molecular transport in cells
-
Elson, E.L. Fluorescence correlation spectroscopy measures molecular transport in cells. Traffic 2001, 2, 789-796.
-
(2001)
Traffic
, vol.2
, pp. 789-796
-
-
Elson, E.L.1
-
184
-
-
31744436399
-
Fluorescence cross-correlation spectroscopy in living cells
-
Bacia, K.; Kim, S.A.; Schwille, P. Fluorescence cross-correlation spectroscopy in living cells. Nat. Methods 2006, 3, 83-89.
-
(2006)
Nat. Methods
, vol.3
, pp. 83-89
-
-
Bacia, K.1
Kim, S.A.2
Schwille, P.3
-
185
-
-
78349292269
-
Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates
-
Stasevich, T.J.; Mueller, F.; Michelman-Ribeiro, A.; Rosales, T.; Knutson, J.R.; McNally, J.G. Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates. Biophys. J. 2010, 99, 3093-3101.
-
(2010)
Biophys. J.
, vol.99
, pp. 3093-3101
-
-
Stasevich, T.J.1
Mueller, F.2
Michelman-Ribeiro, A.3
Rosales, T.4
Knutson, J.R.5
McNally, J.G.6
-
186
-
-
68949108727
-
Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy
-
Michelman-Ribeiro, A.; Mazza, D.; Rosales, T.; Stasevich, T.J.; Boukari, H.; Rishi, V.; Vinson, C.; Knutson, J.R.; McNally, J.G. Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy. Biophys. J. 2009, 97, 337-346.
-
(2009)
Biophys. J.
, vol.97
, pp. 337-346
-
-
Michelman-Ribeiro, A.1
Mazza, D.2
Rosales, T.3
Stasevich, T.J.4
Boukari, H.5
Rishi, V.6
Vinson, C.7
Knutson, J.R.8
McNally, J.G.9
-
187
-
-
79955407832
-
Real-time observation of transcription initiation and elongation on an endogenous yeast gene
-
Larson, D.R.; Zenklusen, D.; Wu, B.; Chao, J.A.; Singer, R.H. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 2011, 332, 475-478.
-
(2011)
Science
, vol.332
, pp. 475-478
-
-
Larson, D.R.1
Zenklusen, D.2
Wu, B.3
Chao, J.A.4
Singer, R.H.5
-
188
-
-
79960630264
-
Central dogma at the single-molecule level in living cells
-
Li, G.W.; Xie, X.S. Central dogma at the single-molecule level in living cells. Nature 2011, 475, 308-315.
-
(2011)
Nature
, vol.475
, pp. 308-315
-
-
Li, G.W.1
Xie, X.S.2
-
189
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
Yu, J.; Xiao, J.; Ren, X.J.; Lao, K.Q.; Xie, X.S. Probing gene expression in live cells, one protein molecule at a time. Science 2006, 311, 1600-1603.
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.J.3
Lao, K.Q.4
Xie, X.S.5
-
190
-
-
0026771275
-
Sliding and intermolecular transfer of the lac repressor: Kinetic perturbation of a reaction intermediate by a distant DNA sequence
-
Ruusala, T.; Crothers, D.M. Sliding and intermolecular transfer of the lac repressor: Kinetic perturbation of a reaction intermediate by a distant DNA sequence. Proc. Natl. Acad. Sci. USA 1992, 89, 4903-4907.
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 4903-4907
-
-
Ruusala, T.1
Crothers, D.M.2
|