Elongational-flow-induced scission of DNA nanotubes in laminar flow

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 82, Issue 4, 2010, Pages

  Hariadi, Rizal F ^a   Yurke, Bernard ^b  

^a California Institute of Technology   (United States)

^b Boise State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOND STRENGTH; CHAIN SCISSION; CONTINUUM HYDRODYNAMICS; CROSSSECTIONAL GEOMETRY; DNA DOUBLE HELICES; DNA DUPLEXES; DNA MECHANICS; DNA NANOTUBES; DNA TRANSITIONS; ELONGATIONAL FLOW; EXPECTED LENGTH; FIRST-PRINCIPLES; FLUID FLOW; FREE PARAMETERS; LENGTH DISTRIBUTIONS; MODEL SYSTEM; MOLECULAR FORCES; POLYMER BONDS; POLYMER FRAGMENTS; SEMIFLEXIBLE POLYMERS; SINGLE MOLECULE LEVEL; SINGLE-STRANDED DNA;

BOND STRENGTH (MATERIALS); FLUORESCENCE MICROSCOPY; LAMINAR FLOW; NANOTUBES; POLYMERS;

DNA;

EID: 78651314838     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.82.046307     Document Type: Article

References (40)

1. B. A. Buchholz, J. M. Zahn, M. Kenward, G. W. Slater, and A. E. Barron, Polymer 45, 1223 (2004). 10.1016/j.polymer.2003.11.051 (Pubitemid 38121334)
2. P. Oefner, S. Hunicke-Smith, L. Chiang, F. Dietrich, J. Mulligan, and R. Davis, Nucleic Acids Res. 24, 3879 (1996). 10.1093/nar/24.20.3879 (Pubitemid 26385316)
3. Y. Thorstenson, S. P. Hunicke-Smith, P. J. Oefner, and R. D. Davis, Genome Res. 8, 848 (1998).
4. M. Quail, in Encyclopedia of the Human Genome, edited by, D. N. Cooper, (Nature Publishing, London, 2003), Vol. 10.
5. T. R. Serio, A. G. Cashikar, A. S. Kowal, G. J. Sawicki, J. J. Moslehi, L. Serpell, M. F. Arnsdorf, and S. L. Lindquist, Science 289, 1317 (2000). 10.1126/science.289.5483.1317 (Pubitemid 30656041)
6. S. R. Collins, A. Douglass, R. D. Vale, and J. S. Weissman, PLoS Biol. 2, e321 (2004). 10.1371/journal.pbio.0020321 (Pubitemid 39532919)
7. A. F. Horn and E. W. Merrill, Nature (London) 312, 140 (1984). 10.1038/312140a0
8. R. Bowman and N. Davidson, Biopolymers 11, 2601 (1972). 10.1002/bip.1972.360111217
9. B. Dancis, Biophys. J. 24, 489 (1978). 10.1016/S0006-3495(78)85396-X
10. J. Odell and A. Keller, J. Polym. Sci., Part B: Polym. Phys. 24, 1889 (1986). 10.1002/polb.1986.090240901
11. T. Q. Nguyen and H.-H. Kausch, Polymer 33, 2611 (1992). 10.1016/0032-3861(92)91145-R
12. J. Odell and M. Taylor, Biopolymers 34, 1483 (1994). 10.1002/bip. 360341106 (Pubitemid 24334356)
13. S. Vanapalli, S. Ceccio, and M. Solomon, Proc. Natl. Acad. Sci. U.S.A. 103, 16660 (2006). 10.1073/pnas.0607933103 (Pubitemid 44737309)
14. J. Larson, Lab Chip 6, 1187 (2006). 10.1039/b602845d (Pubitemid 44290150)
15. P. Yin, R. F. Hariadi, S. Sahu, H. M. T. Choi, S. H. Park, T. H. LaBean, and J. H. Reif, Science 321, 824 (2008). 10.1126/science.1157312
16. R. Schulman and E. Winfree, Proc. Natl. Acad. Sci. U.S.A. 104, 15236 (2007). 10.1073/pnas.0701467104 (Pubitemid 47502902)
17. F. Oosawa and M. Kasai, J. Mol. Biol. 4, 10 (1962). 10.1016/S0022- 2836(62)80112-0
18. S. B. Smith, Y. Cui, and C. Bustamante, Science 271, 795 (1996). 10.1126/science.271.5250.795
19. E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman, Nature (London) 394, 539 (1998). 10.1038/28998 (Pubitemid 28366820)
20. P. W. K. Rothemund, A. Ekani-Nkodo, N. Papadakis, A. Kumar, D. K. Fygenson, and E. Winfree, J. Am. Chem. Soc. 126, 16344 (2004). 10.1021/ja044319l (Pubitemid 40081931)
21. P. W. K. Rothemund, N. Papadakis, and E. Winfree, PLoS Biol. 2, e424 (2004). 10.1371/journal.pbio.0020424 (Pubitemid 40280512)
22. F. A. Aldaye, A. L. Palmer, and H. F. Sleiman, Science 321, 1795 (2008). 10.1126/science.1154533
23. R. H. Wade and D. Chrètien, J. Struct. Biol. 110, 1 (1993). 10.1006/jsbi.1993.1001
24. A. Ekani-Nkodo, A. Kumar, and D. K. Fygenson, Phys. Rev. Lett. 93, 268301 (2004). 10.1103/PhysRevLett.93.268301 (Pubitemid 40213769)
25. T. Fu and N. Seeman, Biochemistry 32, 3211 (1993). 10.1021/bi00064a003
26. V. Bloomfield, D. Crothers, and I. Tinoco, Nucleic Acids: Structures, Properties, and Functions (University Science Books, Sausalito, CA, 2000).
27. B. Tinland, A. Pluen, J. Sturm, and G. Weill, Macromolecules 30, 5763 (1997). 10.1021/ma970381+
28. D. Duffy, J. McDonald, O. Schueller, and G. Whitesides, Anal. Chem. 70, 4974 (1998). 10.1021/ac980656z (Pubitemid 28553167)
29. M. Unger, H. Chou, T. Thorsen, A. Scherer, and S. Quake, Science 288, 113 (2000). 10.1126/science.288.5463.113 (Pubitemid 30203039)
30. I. Braslavsky, B. Hebert, E. Kartalov, and S. Quake, Proc. Natl. Acad. Sci. U.S.A. 100, 3960 (2003). 10.1073/pnas.0230489100 (Pubitemid 36418139)
31. See http://rsbweb.nih.gov/ij/
32. R. G. Larson, T. T. Perkins, D. E. Smith, and S. Chu, Phys. Rev. E 55, 1794 (1997). 10.1103/PhysRevE.55.1794
33. J. Morfill, F. Kuhner, K. Blank, R. A. Lugmaier, J. Sedlmair, and H. E. Gaub, Biophys. J. 93, 2400 (2007). 10.1529/biophysj.107.106112 (Pubitemid 47511140)
34. C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, Curr. Opin. Struct. Biol. 10, 279 (2000). 10.1016/S0959-440X(00)00085-3 (Pubitemid 30333096)
35. C. Radding, K. Beattie, W. Holloman, and R. Wiegand, J. Mol. Biol. 116, 825 (1977). 10.1016/0022-2836(77)90273-X
36. I. Panyutin and P. Hsieh, Proc. Natl. Acad. Sci. U.S.A. 91, 2021 (1994). 10.1073/pnas.91.6.2021
37. B. Yurke and R. F. Hariadi (unpublished).
38. R. Schulman and E. Winfree, Advances in Artificial Life (Springer-Verlag, Berlin, 2005), 734-743.
39. K. D. Knudsen, J. G. H. Cilfre, and J. G. de la Torre, Macromolecules 29, 3603 (1996). 10.1021/ma9513980
40. T. Nguyen and H. Kausch, Macromolecules 23, 5137 (1990). 10.1021/ma00226a017