Understanding the physics of DNA using nanoscale single-molecule manipulation
Eric W. Frey, Ashton A. Gooding, Sitara Wijeratne, Ching-Hwa Kiang
Understanding the physics of DNA using nanoscale single-molecule manipulation
Processes for decoding the genetic information in cells, includingtranscription, replication, recombination and repair, involve thedeformation of DNA from its equilibrium structures such as bending,stretching, twisting, and unzipping of the double helix. Single-moleculemanipulation techniques have made it possible to control DNA conformationand simultaneously detect the induced changes, revealing a rich varietyof mechanically-induced conformational changes and thermodynamic states.These single-molecule techniques helped us to reveal the physics ofDNA and the processes involved in the passing on of the genetic code.
single-molecule manipulation / the physics of DNA
[1] |
M. E. Hogan and R. H. Austin, Nature, 1987, 329(6136): 263
CrossRef
ADS
Google scholar
|
[2] |
S. D. Goodman and H. A. Nash, Nature, 1989, 341(6239): 251
CrossRef
ADS
Google scholar
|
[3] |
A. Stasiak and E. D. Capua, Nature, 1982, 299(5879): 185
CrossRef
ADS
Google scholar
|
[4] |
M. Hegner, S. B. Smith, and C. Bustamante, Proc. Natl. Acad. Sci.USA, 1999, 96(18): 10109
CrossRef
ADS
Google scholar
|
[5] |
D. S. Johnson, L. Bai, B. Y. Smith, S. S. Patel, and M. D. Wang, Cell, 2007, 129(7): 1299
CrossRef
ADS
Google scholar
|
[6] |
V. A. Bloomfield, D. M. Crothers, and I. Tinoco Jr., Nucleic Acids: Structures,Properties, and Functions, Sausalito, California: University ScienceBooks, 2000
|
[7] |
C. G. Baumann, S. B. Smith, V. A. Bloomfield, and C. Bustamante, Proc. Natl. Acad. Sci. USA, 1997, 94(12): 6185
CrossRef
ADS
Google scholar
|
[8] |
D. E. Smith, S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, and C. Bustamante, Nature, 2001, 413(6857): 748
CrossRef
ADS
Google scholar
|
[9] |
D. N. Fuller, D. M. Raymer, V. I. Kottadiel, V. B. Rao, and D. E. Smith, Proc. Natl. Acad. Sci.USA, 2007, 104(43): 16868
CrossRef
ADS
Google scholar
|
[10] |
D. N. Fuller, J. P. Rickgauer, P. J. Jardine, S. Grimes, D. L. Anderson, and D. E. Smith, Proc. Natl. Acad. Sci. USA, 2007, 104(27): 11245
CrossRef
ADS
Google scholar
|
[11] |
G. Felsenfeld and M. Groudine, Nature, 2003, 421(6921): 448
CrossRef
ADS
Google scholar
|
[12] |
B. D. Brower-Toland, C. L. Smith, R. C. Yeh, J. T. Lis, C. L. Peterson, and M. D. Wang, Proc. Natl. Acad. Sci.USA, 2002, 99(4): 1960
CrossRef
ADS
Google scholar
|
[13] |
T. R. Strick, V. Croquette, and D. Bensimon, Nature, 2000, 404(6780): 901
CrossRef
ADS
Google scholar
|
[14] |
E. A. Abbondanzieri, W. J. Greenleaf, J. W. Shaevitz, R. Landick, and S. M. Block, Nature, 2005, 438(7067): 460
CrossRef
ADS
Google scholar
|
[15] |
G. J. L. Wuite, S. B. Smith, M. Young, D. Keller, and C. Bustamante, Nature, 2000, 404(6773): 103
CrossRef
ADS
Google scholar
|
[16] |
K. Luger, A. W. M�der, R. K. Richmond, D. F. Sargent, and T. J. Richmond, Nature, 1997, 389(6648): 251
CrossRef
ADS
Google scholar
|
[17] |
W. D. Volkmuth and R. H. Austin, Nature, 1992, 358(6387): 600
CrossRef
ADS
Google scholar
|
[18] |
J. O. Tegenfeldt, C. Prinz, H. Cao, S. Chou, W. W. Reisner, R. Riehn, Y. M.Wang, E. C. Cox, J. C. Sturm, P. Silberzan, and R. H. Austin, Proc. Natl. Acad. Sci.USA, 2004, 101(30): 10979
CrossRef
ADS
Google scholar
|
[19] |
W. Reisner, K. J. Morton, R. Riehn, Y. M. Wang, Z. Yu, M. Rosen, J. C. Sturm, S. Y. Chou, E. Frey, and R. H. Austin, Phys. Rev. Lett., 2005, 94(19): 196101
CrossRef
ADS
Google scholar
|
[20] |
A. F. Sauer-Budge, J. A. Nyamwanda, D. K. Lubensky, and D. Branton, Phys. Rev. Lett., 2003, 90(23): 238101
CrossRef
ADS
Google scholar
|
[21] |
W.-S. Chen, W.-H. Chen, Z. Chen, A. A. Gooding, K.-J. Lin, and C.-H. Kiang, Phys. Rev. Lett., 2010, 105(21): 218104
CrossRef
ADS
Google scholar
|
[22] |
T. Lionnet, S. Joubaud, R. Lavery, D. Bensimon, and V. Croquette, Phys. Rev. Lett., 2006, 96(17): 178102
CrossRef
ADS
Google scholar
|
[23] |
J. L. Hutter and J. Bechhoefer, Rev. Sci. Instrum., 1993, 64(7): 1868
CrossRef
ADS
Google scholar
|
[24] |
M. Rief, H. Clausen-Schaumann, and H. E. Gaub, Nat. Struct. Biol., 1999, 6(4): 346
CrossRef
ADS
Google scholar
|
[25] |
D. B. Staple, M. Loparic, H. J. Kreuzer, and L. Kreplak, Phys. Rev. Lett., 2009, 102(12): 128302
CrossRef
ADS
Google scholar
|
[26] |
S. Lv, D. M. Dudek, Y. Cao, M. M. Balamurali, J. Gosline, and H. Li, Nature, 2010, 465(7294): 69
CrossRef
ADS
Google scholar
|
[27] |
K. C. Neuman, E. H. Chadd, G. F. Liou, K. Bergman, and S. M. Block, Biophys. J., 1999, 77(5): 2856
CrossRef
ADS
Google scholar
|
[28] |
D. Koirala, S. Dhakal, B. Ashbridge, Y. Sannohe, R. Rodriguez, H. Sugiyama, S. Balasubramanian, and H.Mao, Nat. Chem., 2011, 3(10): 782
CrossRef
ADS
Google scholar
|
[29] |
T. Gibaud, E. Barry, M. J. Zakhary, M. Henglin, A. Ward, Y. Yang, C. Berciu, R. Oldenbourg, M. F. Hagan, D. Nicastro, R. B. Meyer, and Z. Dogic, Nature, 2012, 481(7381): 348
|
[30] |
S. B. Smith, Y. J. Cui, and C. Bustamante, Science, 1996, 271(5250): 795
CrossRef
ADS
Google scholar
|
[31] |
T. Strick, J. Allemand, V. Croquette, and D. Bensimon, Prog. Biophys. Mol. Biol., 2000, 74(1-2): 115
CrossRef
ADS
Google scholar
|
[32] |
J. Lipfert, M. Wiggin, J. W. Kerssemakers, F. Pedaci, and N. H. Dekker, Nat. Commun., 2011, 2: 439
CrossRef
ADS
Google scholar
|
[33] |
T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette, Biophys. J., 1998, 74(4): 2016
CrossRef
ADS
Google scholar
|
[34] |
J. Yan, D. Skoko, and J. F. Marko, Phys. Rev. E, 2004, 70(1): 011905
CrossRef
ADS
Google scholar
|
[35] |
H. Chen, H. Fu, X. Zhu, P. Cong, F. Nakamura, and J. Yan, Biophys. J., 2011, 100(2): 517
CrossRef
ADS
Google scholar
|
[36] |
J. Welker and F. J. Giessibl, Science, 2012, 336(6080): 444
CrossRef
ADS
Google scholar
|
[37] |
J. Stigler, F. Ziegler, A. Gieseke, J. C. M. Gebhardt, and M. Rief, Science, 2011, 334(6055): 512
|
[38] |
A. B�rut, A. Arakelyan, A. Petrosyan, S. Ciliberto, R. Dillenschneider, and E. Lutz, Nature, 2012, 483(7388): 187
CrossRef
ADS
Google scholar
|
[39] |
E. A. Shank, C. Cecconi, J. W. Dill, S. Marqusee, and C. Bustamante, Nature, 2010, 465(7298): 637
CrossRef
ADS
Google scholar
|
[40] |
A. del Rio, R. Perez-Jimenez, R. Liu, P. Roca-Cusachs, J. M. Fernandez, and M. P. Sheetz, Science, 2009, 323(5914): 638
CrossRef
ADS
Google scholar
|
[41] |
Y. Deng, M. Sun, and J. W. Shaevitz, Phys. Rev. Lett., 2011, 107(15): 158101
CrossRef
ADS
Google scholar
|
[42] |
J. van Mameren, P. Gross, G. Farge, P. Hooijman, M. Modesti, M. Falkenberg, G. J. L. Wuite, and E. J. G. Peterman, Proc. Natl. Acad. Sci. USA, 2009, 106(43): 18231
CrossRef
ADS
Google scholar
|
[43] |
M. J. Lang, P. M. Fordyce, A.M. Engh, K. C. Neuman, and S. M. Block, Nat. Methods, 2004, 1(2): 1
CrossRef
ADS
Google scholar
|
[44] |
A. Hards, C. Zhou, M. Seitz, C. Br�uchle, and A. Zumbusch, Chem. Phys. Chem., 2005, 6(3): 534
CrossRef
ADS
Google scholar
|
[45] |
J. F. Marko and E. D. Siggia, Macromolecules, 1995, 28(26): 8759
CrossRef
ADS
Google scholar
|
[46] |
M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, Biophys. J., 1997, 72(3): 1335
CrossRef
ADS
Google scholar
|
[47] |
H. Clausen-Schaumann, M. Rief, C. Tolksdorf, and H. E. Gaub, Biophys. J., 2000, 78(4): 1997
CrossRef
ADS
Google scholar
|
[48] |
S. Cocco, J. Yan, J.-F. L�ger, D. Chatenay, and J. Marko, Phys. Rev. E, 2004, 70(1): 011910
CrossRef
ADS
Google scholar
|
[49] |
C. P. Calderon, W.-H. Chen, K.-J. Lin, N. C. Harris, and C.-H. Kiang, J. Phys.: Condens.Matter, 2009, 21(3): 034114
CrossRef
ADS
Google scholar
|
[50] |
T. Odijk, Macromolecules, 1995, 28(20): 7016
CrossRef
ADS
Google scholar
|
[51] |
P. Cluzel, A. Lebrun, C. Heller, R. Lavery, J.-L. Viovy, D. Chatenay, and F. Caron, Science, 1996, 271(5250): 792
CrossRef
ADS
Google scholar
|
[52] |
H. Fu, H. Chen, J. F. Marko, and J. Yan, NucleicAcids Res., 2010, 38(16): 5594
CrossRef
ADS
Google scholar
|
[53] |
H. Fu, H. Chen, X. Zhang, Y. Qu, J. F. Marko, and J. Yan, Nucleic Acids Res., 2011, 39(8): 3473
CrossRef
ADS
Google scholar
|
[54] |
X. Zhang, H. Chen, H. Fu, P. S. Doyle, and J. Yan, Proc. Natl. Acad. Sci.USA, 2012, 109: 8103
CrossRef
ADS
Google scholar
|
[55] |
C.-H. Ke, M. Humeniuk, H. S-Gracz, and P. E. Marszalek, Phys. Rev. Lett., 2007, 99(1): 018302
CrossRef
ADS
Google scholar
|
[56] |
B. Essevaz-Roulet, U. Bockelmann, and F. Heslot, Proc. Natl. Acad. Sci.USA, 1997, 94(22): 11935
CrossRef
ADS
Google scholar
|
[57] |
C. Danilowicz, V. W. Coljee, C. Bouzigues, D. K. Lubensky, D. R. Nelson, and M. Prentiss, Proc. Natl. Acad. Sci. USA, 2003, 100(4): 1694
CrossRef
ADS
Google scholar
|
[58] |
K. Hatch, C. Danilowicz, V. Coljee, and M. Prentiss, Phys. Rev. E, 2007, 75(5): 051908
CrossRef
ADS
Google scholar
|
/
〈 | 〉 |