Orientational correlations in confined DNA

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

Volumn 86, Issue 4, 2012, Pages

  Werner, E ^a   Persson, F ^a   Westerlund, F ^b   Tegenfeldt, J O ^a,c   Mehlig, B ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^c LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CHANNEL DIAMETERS; DNA CONFORMATIONS; DNA MOLECULES; END-TO-END DISTANCES; LOCAL CORRELATIONS; MONTE CARLO SIMULATION; NANO CHANNELS; ORIENTATIONAL CORRELATIONS; THEORETICAL RESULT;

MEAN FIELD THEORY; MOLECULES; MONTE CARLO METHODS;

DNA;

EID: 84867533563     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.86.041802     Document Type: Article

References (38)

1. D. Marenduzzo, C. Micheletti, and E. Orlandini, J. Phys.: Condens. Matter JCOMEL 0953-8984 10.1088/0953-8984/22/28/283102 22, 283102 (2010).
2. H. Zhou, G. Rivas, and A. Minton, Annu. Rev. Biophys. 1936-122X 10.1146/annurev.biophys.37.032807.125817 37, 375 (2008).
3. S. Köster and T. Pfohl, Cell Motil. Cytoskeleton CMCYEO 0886-1544 10.1002/cm.20336 66, 771 (2009).
4. S. Jun and B. Mulder, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0605305103 103, 12388 (2006). (Pubitemid 44267269)
5. A. Wolffe, Chromatin: Structure and Function (Academic, London, 1998).
6. J. Errington, Microbiol. Rev. 57, 1 (1993).
7. J. A. Speir and J. E. Johnson, Curr. Opin. Struct. Biol. 0959-440X 10.1016/j.sbi.2011.11.002 22, 65 (2012).
8. M. Inamdar, W. Gelbart, and R. Phillips, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.105.070532 91, 411 (2006).
9. D. Löf, K. Schillén, B. Jönsson, and A. Evilevitch, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2007.01.076 368, 55 (2007). (Pubitemid 46441215)
10. C. Baumann, V. Bloomfield, S. Smith, C. Bustamante, M. Wang, and S. Block, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(00)76744-0 78, 1965 (2000).
11. C. Zhang, Z. Gong, D. Guttula, P. Malar, J. van Kan, P. Doyle, and J. Van Der Maarel, J. Phys. Chem. B 1520-5207 10.1021/jp2124907 116, 3031 (2012).
12. F. Persson and J. O. Tegenfeldt, Chem. Soc. Rev. 0306-0012 10.1039/b912918a 39, 985 (2010).
13. S. L. Levy and H. G. Craighead, Chem. Soc. Rev. 0306-0012 10.1039/b820266b 39, 1133 (2010).
14. F. Persson, F. Westerlund, J. O. Tegenfeldt, and A. Kristensen, Small 1613-6810 10.1002/smll.200800423 5, 190 (2009).
15. P. G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979).
16. P. Flory, Principles of Polymer Chemistry (Cornell University Press, Ithaca, NY, 1953).
17. T. Odijk, Macromolecules MAMOBX 0024-9297 10.1021/ma00242a015 16, 1340 (1983).
18. W. Reisner, K. J. Morton, R. Riehn, Y. M. Wang, Z. N. Yu, M. Rosen, J. C. Sturm, S. Y. Chou, E. Frey, and R. H. Austin, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.196101 94, 196101 (2005). (Pubitemid 43272621)
19. P. Cifra, Z. Benkova, and T. Bleha, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp806126r 113, 1843 (2009).
20. Y. Wang, D. R. Tree, and K. D. Dorfman, Macromolecules MAMOBX 0024-9297 10.1021/ma201277e 44, 6594 (2011).
21. F. Persson, P. Utko, W. Reisner, N. B. Larsen, and A. Kristensen, Nano Lett. NALEFD 1530-6984 10.1021/nl803030e 9, 1382 (2009).
22. L. Schäfer, A. Ostendorf, and J. Hager, J. Phys. A JPHAC5 1361-6447 10.1088/0305-4470/32/45/306 32, 7875 (1999).
23. J. P. Wittmer, H. Meyer, J. Baschnagel, A. Johner, S. Obukhov, L. Mattioni, M. Müller, and A. N. Semenov, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.147801 93, 147801 (2004).
24. H. Hsu, W. Paul, and K. Binder, Macromolecules MAMOBX 0024-9297 10.1021/ma902715e 43, 3094 (2010).
25. F. Wagner, G. Lattanzi, and E. Frey, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.75.050902 75, 050902 (2007).
26. P. Cifra, Z. Benková, and T. Bleha, PhysChemChemPhys PPCPFQ 1463-9076 10.1039/b923598a 12, 8934 (2010).
27. M. Choi, C. Santangelo, O. Pelletier, J. Kim, S. Kwon, Z. Wen, Y. Li, P. Pincus, C. Safinya, and M. Kim, Macromolecules MAMOBX 0024-9297 10.1021/ma051348n 38, 9882 (2005). (Pubitemid 41698441)
28. S. Köster, J. Kierfeld, and T. Pfohl, Eur. Phys. J. E EPJSFH 1292-8941 10.1140/epje/i2007-10312-3 25, 439 (2008).
29. D. Yoon, M. Vacatello, and G. Smith, in Monte Carlo and Molecular Dynamics Simulations in Polymer Science, edited by, K. Binder, (Oxford University Press, New York, 1995).
30. T. Odijk, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2400227 125, 204904 (2006). (Pubitemid 44847707)
31. L. Onsager, Ann. NY Acad. Sci. ANYAA9 0077-8923 10.1111/j.1749-6632.1949. tb27296.x 51, 627 (1949).
32. P. Cifra, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3271830 131, 224903 (2009).
33. See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevE.86.041802 for experimental details.
34. C. Murade, V. Subramaniam, C. Otto, and M. Bennink, Biophys. J. BIOJAU 0006-3495 10.1016/j.bpj.2009.05.024 97, 835 (2009).
35. C. Murade, V. Subramaniam, C. Otto, and M. Bennink, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkq034 38, 3423 (2010).
36. I. Vladescu, M. McCauley, M. Nuñez, I. Rouzina, and M. Williams, Nat. Methods 1548-7091 10.1038/nmeth1044 4, 517 (2007). (Pubitemid 46852078)
37. K. Günther, M. Mertig, and R. Seidel, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkq434 38, 6526 (2010).
38. F. Persson, P. Bingen, T. Staudt, J. Engelhardt, J. O. Tegenfeldt, and S. Hell, Angew. Chem. Int. Ed. 1433-7851 10.1002/anie.201100371 50, 5581 (2011).