메뉴 건너뛰기




Volumn 14, Issue 2, 2013, Pages 3961-3992

Optical methods to study protein-DNA interactions in vitro and in living cells at the single-molecule level

Author keywords

Combining single molecule fluorescence and optical trapping; DNA curtains; Facilitated diffusion; In vivo transcription factors dynamics; Magnetic tweezers; Optical tweezers; Protein DNA interactions; Single molecule imaging; Single molecule techniques; Tethered particle motion

Indexed keywords

DNA; DNA BOUND FLUORESCENT PROTEIN; FLUORESCENT DYE; QUANTUM DOT; UNCLASSIFIED DRUG;

EID: 84875090408     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms14023961     Document Type: Review
Times cited : (59)

References (190)
  • 1
    • 77649111696 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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
  • 27
    • 49449107340 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 31
    • 34347240880 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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
  • 36
    • 23244442263 scopus 로고    scopus 로고
    • 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
  • 38
    • 33746207766 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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
  • 43
    • 54749084305 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 48
    • 66249111861 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 52
    • 33749359386 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 58
    • 77954571156 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 71
    • 0001767132 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 75
    • 34250766751 scopus 로고    scopus 로고
    • 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
  • 77
    • 0141534308 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 80
    • 33846411048 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 88
    • 70949101796 scopus 로고    scopus 로고
    • 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
  • 90
    • 80053144268 scopus 로고    scopus 로고
    • 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
  • 92
    • 33847672227 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 97
    • 77955629227 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 101
    • 43349099320 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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
  • 106
    • 0037438725 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 111
    • 66149144002 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 116
    • 34547138714 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 120
    • 34249932435 scopus 로고    scopus 로고
    • 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
  • 122
    • 33645807371 scopus 로고    scopus 로고
    • 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
  • 128
    • 0018472170 scopus 로고
    • 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
  • 130
    • 79952494759 scopus 로고    scopus 로고
    • 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
  • 133
    • 77955416347 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 137
    • 0141540814 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 147
    • 0035909370 scopus 로고    scopus 로고
    • 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
  • 150
    • 0034602688 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 154
    • 79953873168 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 157
    • 59649116344 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 160
    • 2642522184 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 168
    • 0036231415 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 179
    • 0037049641 scopus 로고    scopus 로고
    • 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
  • 181
  • 182
    • 0032828419 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 187
    • 79955407832 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.