DNA motion capture reveals the mechanical properties of DNA at the mesoscale

Biophysical Journal

Volumn 108, Issue 10, 2015, Pages 2532-2540

  Price, Allen C ^a   Pilkiewicz, Kevin R ^b   Graham, Thomas G W ^c   Song, Dan ^c   Eaves, Joel D ^b   Loparo, Joseph J ^c  

^a EMMANUEL COLLEGE   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

CHEMISTRY; ELASTICITY; MOTION;

DNA, BACTERIAL; ELASTICITY; MOTION;

EID: 84930011873     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2015.04.022     Document Type: Article

References (38)

1. G. Yu, and A. Kushwaha Z. Bao The shear flow processing of controlled DNA tethering and stretching for organic molecular electronics ACS Nano 5 2011 275 282
2. H. Yan, and X. Zhang N.C. Seeman A robust DNA mechanical device controlled by hybridization topology Nature 415 2002 62 65
3. C. Bustamante, W. Cheng, and Y.X. Mejia Revisiting the central dogma one molecule at a time Cell 144 2011 480 497
4. J.F. Marko, and E.D. Siggia Stretching DNA Macromolecules 28 1995 8759 8770
5. S.R. Aragón, and R. Pecora Dynamics of wormlike chains Macromolecules 18 1985 1868 1875
6. C. Bustamante, and J.F. Marko S. Smith Entropic elasticity of λ-phage DNA Science 265 1994 1599 1600
7. J. Kindt, and S. Tzlil W.M. Gelbart DNA packaging and ejection forces in bacteriophage Proc. Natl. Acad. Sci. USA 98 2001 13671 13674
8. J. Yan, and J.F. Marko Effects of DNA-distorting proteins on DNA elastic response Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 68 2003 011905
9. J. van Noort, and S. Verbrugge R.T. Dame Dual architectural roles of HU: formation of flexible hinges and rigid filaments Proc. Natl. Acad. Sci. USA 101 2004 6969 6974
10. C. Bustamante, and S.B. Smith D. Smith Single-molecule studies of DNA mechanics Curr. Opin. Struct. Biol. 10 2000 279 285
11. C. Bustamante, Z. Bryant, and S.B. Smith Ten years of tension: single-molecule DNA mechanics Nature 421 2003 423 427
12. P.E. Rouse Jr. A theory of the linear viscoelastic properties of dilute solutions of coiling polymers J. Chem. Phys. 21 1953 1272 1280
13. Y. Marciano, and F. Brochard-Wyart Normal modes of stretched polymer chains Macromolecules 28 1995 985 990
14. B.H. Zimm, and J.K. Bragg Theory of the phase transition between helix and random coil in polypeptide chains J. Chem. Phys. 31 1959 526 535
15. Y. Seol, and J. Li M.D. Betterton Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 μm Biophys. J. 93 2007 4360 4373
16. R. Vafabakhsh, and T. Ha Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization Science 337 2012 1097 1101
17. P.A. Wiggins, and T. van der Heijden P.C. Nelson High flexibility of DNA on short length scales probed by atomic force microscopy Nat. Nanotechnol. 1 2006 137 141
18. A.E. Cohen, and W.E. Moerner Principal-components analysis of shape fluctuations of single DNA molecules Proc. Natl. Acad. Sci. USA 104 2007 12622 12627
19. K. King, S.J. Benkovic, and P. Modrich Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease J. Biol. Chem. 264 1989 11807 11815
20. I.J. Finkelstein, M.-L. Visnapuu, and E.C. Greene Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase Nature 468 2010 983 987
21. R.E. Thompson, D.R. Larson, and W.W. Webb Precise nanometer localization analysis for individual fluorescent probes Biophys. J. 82 2002 2775 2783
22. P.S. Doyle, B. Ladoux, and J.L. Viovy Dynamics of a tethered polymer in shear flow Phys. Rev. Lett. 84 2000 4769 4772
23. C.A. Lueth, and E.S.G. Shaqfeh Experimental and numerical studies of tethered DNA shear dynamics in the flow-gradient plane Macromolecules 42 2009 9170 9182
24. B. Ladoux, and P.S. Doyle Stretching tethered DNA chains in shear flow Europhys. Lett. 52 2000 511 517
25. T.T. Perkins, and D.E. Smith S. Chu Stretching of a single tethered polymer in a uniform flow Science 268 1995 83 87
26. J.-C. Meiners, and S.R. Quake Femtonewton force spectroscopy of single extended DNA molecules Phys. Rev. Lett. 84 2000 5014 5017
27. A. Crut, and D. Lasne P. Desbiolles Transverse fluctuations of single DNA molecules attached at both extremities to a surface Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 67 2003 051910
28. J.W. Hatfield, and S.R. Quake Dynamic properties of an extended polymer in solution Phys. Rev. Lett. 82 1999 3548 3551
29. S. Plimpton Fast parallel algorithms for short-range molecular dynamics J. Comput. Phys. 117 1995 1 19
30. M.D. Wang, and H. Yin S.M. Block Stretching DNA with optical tweezers Biophys. J. 72 1997 1335 1346
31. T.A. Knotts 4th, and N. Rathore J.J. de Pablo A coarse grain model for DNA J. Chem. Phys. 126 2007 084901
32. S. Brinkers, and H.R.C. Dietrich B. Rieger The persistence length of double stranded DNA determined using dark field tethered particle motion J. Chem. Phys. 130 2009 215105
33. P.T. Underhill, and P.S. Doyle On the coarse-graining of polymers into bead-spring chains J. Nonnewton Fluid Mech. 122 2004 3 31
34. O. Hallatschek, E. Frey, and K. Kroy Propagation and relaxation of tension in stiff polymers Phys. Rev. Lett. 94 2005 077804
35. K. Laube, K. Günther, and M. Mertig Analysis of the fluctuations of a single-tethered, quantum-dot labeled DNA molecule in shear flow J. Phys. Condens. Matter 23 2011 184119
36. A. Tafvizi, and F. Huang A.M. van Oijen A single-molecule characterization of p53 search on DNA Proc. Natl. Acad. Sci. USA 108 2011 563 568
37. T.G.W. Graham, and X. Wang J.J. Loparo ParB spreading requires DNA bridging Genes Dev. 28 2014 1228 1238
38. D. Song, and B. Mousley A.C. Price Tethered particle motion with single DNA molecules Am. J. Phys. 83 2015 418