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Volumn 11, Issue 4, 2014, Pages 456-462

Gold rotor bead tracking for high-speed measurements of DNA twist, torque and extension

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); DNA Z; GOLD; GOLD NANOPARTICLE; NUCLEOPROTEIN;

EID: 84897954099     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2854     Document Type: Article
Times cited : (75)

References (56)
  • 2
    • 44449087047 scopus 로고    scopus 로고
    • Single-molecule force spectroscopy: Optical tweezers, magnetic tweezers and atomic force microscopy
    • Neuman, K.C. & Nagy, A. Single-molecule force spectroscopy: Optical tweezers, magnetic tweezers and atomic force microscopy. Nat. Methods 5, 491-505 (2008
    • (2008) Nat. Methods , vol.5 , pp. 491-505
    • Neuman, K.C.1    Nagy, A.2
  • 3
    • 84862615458 scopus 로고    scopus 로고
    • 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. 22, 304 -312 (2012
    • (2012) Curr. Opin. Struct. Biol , vol.22 , pp. 304-312
    • Bryant, Z.1    Oberstrass, F.C.2    Basu, A.3
  • 4
    • 67650354846 scopus 로고    scopus 로고
    • Determining protein-induced DNA bending in force-extension experiments: Theoretical analysis
    • Vologodskii, A. Det ermining protein-induced DNA bending in force-extension experiments: Theoretical analysis. Biophys. J. 96, 3591-3599 (2009
    • (2009) Biophys. J , vol.96 , pp. 3591-3599
    • Vologodskii, A.1
  • 5
    • 34247350048 scopus 로고    scopus 로고
    • Thirty years of Escherichia coli DNA gyrase: From in vivo function to single-molecule mechanism
    • Nollmann, M., Crisona, N.J. & Arimondo, P.B. Thirty years of Escher ichia coli DNA gyrase: From in vivo function to single-molecule mechanism. Biochimie 89, 490-499 (2007
    • (2007) Biochimie , vol.89 , pp. 490-499
    • Nollmann, M.1    Crisona, N.J.2    Arimondo, P.B.3
  • 6
    • 84860751723 scopus 로고    scopus 로고
    • ATP Binding Controls Distinct Structural Transitions of Escherichia Coli DNA Gyrase in Complex with DNA
    • Basu, A., Schoeffler, A.J., Berger, J.M. & Bryant, Z. ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA. Nat. Struct. Mol. Biol. 19, 538-546 (2012
    • (2012) Nat. Struct. Mol. Biol , vol.19 , pp. 538-546
    • Basu, A.1    Schoeffler, A.J.2    Berger, J.M.3    Bryant, Z.4
  • 7
    • 30144434477 scopus 로고    scopus 로고
    • Mechanochemical analysis of DNA gyrase using rotor bead tracking
    • Gore, J. et al. Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature 439, 100-104 (2006
    • (2006) Nature , vol.439 , pp. 100-104
    • Gore, J.1
  • 9
    • 33751218319 scopus 로고    scopus 로고
    • Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
    • Revyakin, A., Liu, C., Ebright, R.H. & Strick, T.R. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314, 1139-1143 (2006
    • (2006) Science , vol.314 , pp. 1139-1143
    • Revyakin, A.1    Liu, C.2    Ebright, R.H.3    Strick, T.R.4
  • 10
    • 84881493788 scopus 로고    scopus 로고
    • Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament
    • Lee, M., Lipfert, J., Sanchez, H., Wyman, C. & Dekker, N.H. Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament. Nucleic Acids Res. 41, 7023- 7030 (2013
    • (2013) Nucleic Acids Res , vol.41 , pp. 7023-7030
    • Lee, M.1    Lipfert, J.2    Sanchez, H.3    Wyman, C.4    Dekker, N.H.5
  • 11
    • 73349112609 scopus 로고    scopus 로고
    • Direct observation of twisting steps during Rad51 polymerization on DNA
    • Arata, H. et al. Direct observation of twisting steps during Rad51 polymerization on DNA. Proc. Natl. Acad. Sci. USA 106, 19239-19244 (2009
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 19239-19244
    • Arata, H.1
  • 12
    • 80052404576 scopus 로고    scopus 로고
    • Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids
    • Lipfert, J., Wiggin M., Kerssemakers, J.W., Pedaci, F. & Dekker, N.H. Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids. Nat. Commun. 2, 439 (2011
    • (2011) Nat. Commun , vol.2 , pp. 439
    • Lipfert, J.1    Wiggin, M.2    Kerssemakers, J.W.3    Pedaci, F.4    Dekker, N.H.5
  • 13
    • 50649101663 scopus 로고    scopus 로고
    • DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology
    • Schoeffler, A.J. & Berger, J.M. DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology. Q. Rev. Biophys. 41, 41-101 (2008
    • (2008) Q. Rev. Biophys , vol.41 , pp. 41-101
    • Schoeffler, A.J.1    Berger, J.M.2
  • 14
    • 0035804245 scopus 로고    scopus 로고
    • Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase
    • Harada, Y. et al. Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase. Nature 409, 113-115 (2001
    • (2001) Nature , vol.409 , pp. 113-115
    • Harada, Y.1
  • 19
    • 0041305824 scopus 로고    scopus 로고
    • Structural transitions and elasticity from torque measurements on DNA
    • Bryant, Z. et al. Structural transitions and elasticity from torque measurements on DNA. Nature 424, 338-341 (2003
    • (2003) Nature , vol.424 , pp. 338-341
    • Bryant, Z.1
  • 20
    • 84863856881 scopus 로고    scopus 로고
    • Electromagnetic torque tweezers: A versatile approach for measurement of single-molecule twist and torque
    • Janssen, X.J. et al. Electromagnetic torque tweezers: A versatile approach for measurement of single-molecule twist and torque. Nano Lett. 12, 3634 -3639 (2012
    • (2012) Nano Lett , vol.12 , pp. 3634-3639
    • Janssen, X.J.1
  • 21
    • 78649709362 scopus 로고    scopus 로고
    • Magnetic torque tweezers: Measuring torsional stiffness in DNA and Rec A-DNA filaments
    • Lipfert, J., Kerssemakers, J.W., Jager, T. & Dekker, N.H. Magnetic torque tweezers: Measuring torsional stiffness in DNA and Rec A-DNA filaments. Nat. Methods 7, 977-980 (2010
    • (2010) Nat. Methods , vol.7 , pp. 977-980
    • Lipfert, J.1    Kerssemakers, J.W.2    Jager, T.3    Dekker, N.H.4
  • 22
    • 84860012641 scopus 로고    scopus 로고
    • Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA
    • Oberstrass, F.C., Fernandes, L.E. & Bryant, Z. Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA. Proc. Natl. Acad. Sci. USA 109, 6106- 6111 (2012
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 6106-6111
    • Oberstrass, F.C.1    Fernandes, L.E.2    Bryant, Z.3
  • 23
    • 41949110996 scopus 로고    scopus 로고
    • Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules
    • Forth, S. et al. Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules. Phys. Rev. Lett. 100, 148301 (2008
    • (2008) Phys. Rev. Lett , vol.100 , pp. 148301
    • Forth, S.1
  • 24
    • 65249161305 scopus 로고    scopus 로고
    • Magnetic tweezers measurement of single molecule torque
    • Celedon, A. et al. Magnetic tweezers measurement of single molecule torque. Nano Lett. 9, 1720-1725 (2009
    • (2009) Nano Lett , vol.9 , pp. 1720-1725
    • Celedon, A.1
  • 25
    • 84877750899 scopus 로고    scopus 로고
    • Torque Spectroscopy of DNA: Base-Pair Stability, Boundary Effects, Backbending, and Breathing Dynamics
    • Oberstrass, F.C., Fernandes, L.E., Lebel, P. & Bryant, Z. Torque Spectroscopy of DNA: Base-Pair Stability, Boundary Effects, Backbending, and Breathing Dynamics. Phys. Rev. Lett. 110, 178103 (2013
    • (2013) Phys. Rev. Lett , vol.110 , pp. 178103
    • Oberstrass, F.C.1    Fernandes, L.E.2    Lebel, P.3    Bryant, Z.4
  • 26
    • 33745823112 scopus 로고    scopus 로고
    • Mechanisms of helicases
    • Patel, S.S. & Donmez, I. Mechanisms of helicases. J. Biol. Chem. 281, 18265-18268 (2006
    • (2006) J. Biol. Chem , vol.281 , pp. 18265-18268
    • Patel, S.S.1    Donmez, I.2
  • 27
    • 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 4, 223-225 (2007
    • (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
  • 28
    • 0030886377 scopus 로고    scopus 로고
    • Proteins unfold in steps
    • Zocchi, G. Proteins unfold in steps. Proc. Natl. Acad. Sci. USA 94, 10647-10651 (1997
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 10647-10651
    • Zocchi, G.1
  • 29
    • 67650391229 scopus 로고    scopus 로고
    • Mechanical characterization of protein L in the low-force regime by electromagnetic tweezers/evanescent nanometry
    • Liu, R., Garcia-Manyes, S., Sarkar, A., Badilla, C.L. & Fernandez, J.M. Mechanical characterization of protein L in the low-force regime by electromagnetic tweezers/evanescent nanometry. Biophys. J. 96, 3810-3821 (2009
    • (2009) Biophys. J , vol.96 , pp. 3810-3821
    • Liu, R.1    Garcia-Manyes, S.2    Sarkar, A.3    Badilla, C.L.4    Fernandez, J.M.5
  • 30
    • 0035912221 scopus 로고    scopus 로고
    • Resolution of distinct rotational substeps by submillisecond kinetic analy sis of F1-ATPase
    • Yasuda, R., Noji, H., Yoshida, M., Kinosita, K. Jr. & Itoh, H. Resolution of distinct rotational substeps by submillisecond kinetic analy sis of F1-ATPase. Nature 410, 898-904 (2001
    • (2001) Nature , vol.410 , pp. 898-904
    • Yasuda, R.1    Noji, H.2    Yoshida, M.3    Kinosita Jr., K.4    Itoh, H.5
  • 31
    • 33847680889 scopus 로고    scopus 로고
    • Dynamics of the unbound head during myosin v processive translocation
    • Dunn, A.R. & Spudich, J.A. Dynamics of the unbound head during myosin V processive translocation. Nat. Struct. Mol. Biol. 14, 246-248 (2007
    • (2007) Nat. Struct. Mol. Biol , vol.14 , pp. 246-248
    • Dunn, A.R.1    Spudich, J.A.2
  • 32
    • 79951714745 scopus 로고    scopus 로고
    • Force-free measurements of the conformations of DNA molecules tethered to a wall
    • Lindner, M. et al. Force-free measurements of the conformations of DNA molecules tethered to a wall. Phys. Rev. E 83, 011916 (2011
    • (2011) Phys. Rev E. , vol.83 , pp. 011916
    • Lindner, M.1
  • 33
    • 77952262873 scopus 로고    scopus 로고
    • Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution
    • Ueno, H. et al. Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution. Biophys. J. 98, 2014 -2023 (2010
    • (2010) Biophys. J , vol.98 , pp. 2014-2023
    • Ueno, H.1
  • 34
    • 77952393147 scopus 로고    scopus 로고
    • Contribution of the myosin VI tail domain to processive stepping and intramolecular tension sensing
    • Dunn, A.R., Chuan, P., Bryant, Z. & Spudich, J.A. Contri bution of the myosin VI tail domain to processive stepping and intramolecular tension sensing. Proc. Natl. Acad. Sci. USA 107, 7746-7750 (2010
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 7746-7750
    • Dunn, A.R.1    Chuan, P.2    Bryant, Z.3    Spudich, J.A.4
  • 35
    • 0038159959 scopus 로고    scopus 로고
    • Objective-type dark-field illumination for scattering from microbeads
    • Braslavsky, I. et al. Objective-type dark-field illumination for scattering from microbeads. Appl. Opt. 40, 5650-5657 (2001
    • (2001) Appl. Opt , vol.40 , pp. 5650-5657
    • Braslavsky, I.1
  • 36
    • 0037330690 scopus 로고    scopus 로고
    • Visualizing single molecules inside living cells using total internal reflection fluorescence microscopy
    • Mashanov, G.I., Tacon, D., Knight, A.E., Peckham, M. & Molloy, J.E. Visualizing single molecules inside living cells using total internal reflection fluorescence microscopy. Methods 29, 142-152 (2003
    • (2003) Methods , vol.29 , pp. 142-152
    • Mashanov, G.I.1    Tacon, D.2    Knight, A.E.3    Peckham, M.4    Molloy, J.E.5
  • 37
    • 33746743013 scopus 로고    scopus 로고
    • Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence
    • Friedman, L.J., Chung, J. & Gelles, J. Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence. Biophys. J. 91, 1023-1031 (2006
    • (2006) Biophys. J , vol.91 , pp. 1023-1031
    • Friedman, L.J.1    Chung, J.2    Gelles, J.3
  • 38
    • 33845467792 scopus 로고    scopus 로고
    • The effect of integration time on fluctuation measurements: Calibrating an optical trap in the presence of motion blur
    • Wong, W.P. & Halvorsen, K. The effect of integration time on fluctuation measurements: Calibrating an optical trap in the presence of motion blur. Opt. Express 14, 12517-12531 (2006
    • (2006) Opt. Express , vol.14 , pp. 12517-12531
    • Wong, W.P.1    Halvorsen, K.2
  • 39
    • 0030601791 scopus 로고    scopus 로고
    • Direct measurement of the torsional rigidity of single actin filaments
    • Yasuda, R., Miyata, H. & Kinosita, K. Jr. Direct measurement of the torsional rigidity of single actin filaments. J. Mol. Biol. 263, 227-236 (1996
    • (1996) J. Mol. Biol , vol.263 , pp. 227-236
    • Yasuda, R.1    Miyata, H.2    Kinosita Jr., K.3
  • 40
    • 33747461393 scopus 로고    scopus 로고
    • DNA overwinds when stretched
    • Gore, J. et al. DNA overwinds when stretched. Nature 442, 836-839 (2006
    • (2006) Nature , vol.442 , pp. 836-839
    • Gore, J.1
  • 42
    • 68849118253 scopus 로고    scopus 로고
    • Twist-stretch coupling and phase transition during DNA supercoiling
    • Sheinin, M.Y. & Wang, M.D. Twist-stretch coupling and phase transition during DNA supercoiling. Phys. Chem. Chem. Phys. 11, 4800-4803 (2009
    • (2009) Phys. Chem. Chem. Phys , vol.11 , pp. 4800-4803
    • Sheinin, M.Y.1    Wang, M.D.2
  • 43
  • 45
    • 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. 92, 190801 (2004
    • (2004) Phys. Rev. Lett , vol.92 , pp. 190801
    • La Porta, A.1    Wang, M.D.2
  • 46
    • 83655192457 scopus 로고    scopus 로고
    • Direct mechanical measurements reveal the material properties of three-dimensional DNA origami
    • Kauert, D.J., Kurth, T., Liedl, T. & Seidel, R. Direct mechanical measurements reveal the material properties of three-dimensional DNA origami. Nano Lett. 11, 5558-5563 (2011
    • (2011) Nano Lett , vol.11 , pp. 5558-5563
    • Kauert, D.J.1    Kurth, T.2    Liedl, T.3    Seidel, R.4
  • 47
    • 84880340824 scopus 로고    scopus 로고
    • Rigid DNA beams for high-resolution single-molecule mechanics
    • Pfitzner, E. et al. Rigid DNA beams for high-resolution single-molecule mechanics. Angew. Chem. Int. Edn Engl. 52, 7766 -7771 (2013
    • (2013) Angew. Chem. Int. Edn Engl , vol.52 , pp. 7766-7771
    • Pfitzner, E.1
  • 48
    • 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 8, 335 -340 (2011
    • (2011) Nat. Methods , vol.8 , pp. 335-340
    • Comstock, M.J.1    Ha, T.2    Chemla, Y.R.3
  • 49
    • 57049139281 scopus 로고    scopus 로고
    • Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution
    • Huang, B., Jones, S.A., Brandenburg, B. & Zhuang, X. Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution. Nat. Methods 5, 1047-1052 (2008
    • (2008) Nat. Methods , vol.5 , pp. 1047-1052
    • Huang, B.1    Jones, S.A.2    Brandenburg, B.3    Zhuang, X.4
  • 50
    • 68949105584 scopus 로고    scopus 로고
    • Quantitative modeling and optimization of magnetic tweezers
    • Lipfert, J., Hao, X. & Dekker, N.H. Quantitative modeling and optimization of magnetic tweezers. Biophys. J. 96, 5040-5049 (2009
    • (2009) Biophys. J , vol.96 , pp. 5040-5049
    • Lipfert, J.1    Hao, X.2    Dekker, N.H.3
  • 51
    • 84861534674 scopus 로고    scopus 로고
    • Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity
    • Tretter, E.M. & Berger, J.M. Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity. J. Biol. Chem. 287, 18636 -18644 (2012
    • (2012) J. Biol. Chem , vol.287 , pp. 18636-18644
    • Tretter, E.M.1    Berger, J.M.2
  • 52
    • 84944485718 scopus 로고
    • Mathematical analysis of random noise
    • Rice, S. Mathematical analysis of random noise. Bell Syst. Tech. J. 24, 46-156 (1945
    • (1945) Bell Syst. Tech. J , vol.24 , pp. 46-156
    • Rice, S.1
  • 54
    • 77958197520 scopus 로고    scopus 로고
    • Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data
    • te Velthuis, A.J., Kerssemakers, J.W., Lipfert, J. & Dekker, N.H. Quantitative guidelines for force calibration t hrough spectral analysis of magnetic tweezers data. Biophys. J. 99, 1292-1302 (2010
    • (2010) Biophys. J , vol.99 , pp. 1292-1302
    • Te Velthuis, A.J.1    Kerssemakers, J.W.2    Lipfert, J.3    Dekker, N.H.4
  • 55
    • 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. 82, 3314-3329 (2002
    • (2002) Biophys. J , vol.82 , pp. 3314-3329
    • Gosse, C.1    Croquette, V.2
  • 56
    • 59149096327 scopus 로고    scopus 로고
    • Torsional stiffness of single superparamagnetic microspheres in an external magnetic field
    • Klaue, D. & Seidel, R. Torsional stiffness of single superparamagnetic microspheres in an external magnetic field. Phys. Rev. Lett. 102, 028302 (2009
    • (2009) Phys. Rev. Lett , vol.102 , pp. 028302
    • Klaue, D.1    Seidel, R.2


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