Full-text resources of PSJD and other databases are now available in the new Library of Science.
Visit https://bibliotekanauki.pl

PL EN


Preferences help
enabled [disable] Abstract
Number of results

Journal

2010 | 8 | 6 | 883-892

Article title

Simulation of dissociation of DNA duplexes attached to the surface

Content

Title variants

Languages of publication

EN

Abstracts

EN
We present Monte Carlo simulations of dissociation of duplexes formed of complementary single-stranded DNAs with one of the strands attached to the surface. To describe the transition from the bound state to the unbound state of two strands located nearby, we use a lattice model taking DNA base-pair interactions and comformational changes into account. The results obtained are employed as a basis for a more coarse-grained model including strand backward association and diffusion resulting in complete dissociation. The distribution of the dissociation time is found to be exponential. This finding indicates that the non-exponential kinetic features observed in the corresponding experiments seem to be related to extrinsic factors, e.g., to the surface heterogeneity.

Publisher

Journal

Year

Volume

8

Issue

6

Pages

883-892

Physical description

Dates

published
1 - 12 - 2010
online
5 - 9 - 2010

Contributors

  • Division of Biological Physics, Department of Applied Physics, Chalmers University of Technology, S-41296, Göteborg, Sweden
  • Division of Biological Physics, Department of Applied Physics, Chalmers University of Technology, S-41296, Göteborg, Sweden

References

  • [1] K. A. Dill, S. B. Ozkan, M. S. Shell, T. R. Weikl, Ann. Rev. Biophys. 37, 289 (2008) http://dx.doi.org/10.1146/annurev.biophys.37.092707.153558[Crossref]
  • [2] A. Borgia, P. M. Williams, and J. Clarke, Annu. Rev. Biochem. 77, 101 (2008) http://dx.doi.org/10.1146/annurev.biochem.77.060706.093102[Crossref]
  • [3] A. V. Finkelstein, O. V. Galzitskaya, Phys. Life Rev. 1, 23 (2004) http://dx.doi.org/10.1016/j.plrev.2004.03.001[Crossref]
  • [4] V. P. Zhdanov, B. Kasemo, Proteins 42, 481 (2001) http://dx.doi.org/10.1002/1097-0134(20010301)42:4<481::AID-PROT70>3.0.CO;2-N[Crossref]
  • [5] D. Poland, H. A. Scheraga, J. Chem. Phys. 45, 1456 (1966) http://dx.doi.org/10.1063/1.1727785[Crossref]
  • [6] D. Poland, H. A. Scheraga, J. Chem. Phys. 45, 1464 (1966) http://dx.doi.org/10.1063/1.1727786[Crossref]
  • [7] D. Poland, H. A. Scheraga, J. Chem. Phys. 45, 2071 (1966) http://dx.doi.org/10.1063/1.1727893[Crossref]
  • [8] H. A. Scheraga, J. A. Vila, D. R. Ripoll, Biophys. Chem. 101–102, 255 (2002) http://dx.doi.org/10.1016/S0301-4622(02)00175-8[Crossref]
  • [9] C. Richard, A. J. Guttmann, J. Stat. Phys. 115, 925 (2004) http://dx.doi.org/10.1023/B:JOSS.0000022370.48118.8b[Crossref]
  • [10] D. Marenduzzo, S. M. Bhattacharjee, A. Maritan, E. Orlandini, F. Seno, Phys. Rev. Lett. 88, 028102 (2001) http://dx.doi.org/10.1103/PhysRevLett.88.028102[Crossref]
  • [11] S. Ares, N. K. Voulgarakis, K. O. Rasmussen, A. R. Bishop, Phys. Rev. Lett. 94, 035504 (2005) http://dx.doi.org/10.1103/PhysRevLett.94.035504[Crossref]
  • [12] B. Coluzzi, Phys. Rev. E 73, 011911 (2006) http://dx.doi.org/10.1103/PhysRevE.73.011911[Crossref]
  • [13] S. Ares, A. Sanchez, Eur. Phys. J. B 56, 253 (2007) http://dx.doi.org/10.1140/epjb/e2007-00112-9[Crossref]
  • [14] A. Bar, Y. Kafri, D. Mukamel, Phys. Rev. Lett. 98, 038103 (2007) http://dx.doi.org/10.1103/PhysRevLett.98.038103[Crossref]
  • [15] H. C. Fogedby, R. Metzler, Phys. Rev. Lett. 98, 070601 (2007) http://dx.doi.org/10.1103/PhysRevLett.98.070601[Crossref]
  • [16] J. Palmeri, M. Manghi, N. Destainville, Phys. Rev. Lett. 99, 088103 (2007) http://dx.doi.org/10.1103/PhysRevLett.99.088103[Crossref]
  • [17] J.-Y. Kim, J.-H. Jeon, W. Sung, J. Chem. Phys. 128, 055101 (2008) http://dx.doi.org/10.1063/1.2827471[Crossref]
  • [18] F. D. L. Santos, O. Al Hammal, M. A. Munoz, Phys. Rev. E 77, 032901 (2008) http://dx.doi.org/10.1103/PhysRevE.77.032901[Crossref]
  • [19] B. Alexandrov, N. K. Voulgarakis, K. Rasmussenl, A. Usheva, A. R. Bishop, J. Phys.-Condens. Mat. 21, 034107 (2009) http://dx.doi.org/10.1088/0953-8984/21/3/034107[Crossref]
  • [20] A. Bar, Y. Kafri, D. Mukamel, J. Phys.-Condens. Mat. 21, 034110 (2009) http://dx.doi.org/10.1088/0953-8984/21/3/034110[Crossref]
  • [21] E. J. Sambriski, V. Ortiz, J. J. de Pablo; J. Phys.-Condens. Mat. 21, 034105 (2009) http://dx.doi.org/10.1088/0953-8984/21/3/034105[Crossref]
  • [22] A. E. Allahverdyan, Z. S. Gevorkian, C.-K. Hu, T. M. Nieuwenhuizen, Phys. Rev. E. 79, 031903 (2009) http://dx.doi.org/10.1103/PhysRevE.79.031903[Crossref]
  • [23] R. Kapria, J. Chem. Phys. 130, 145105 (2009) http://dx.doi.org/10.1063/1.3116082[Crossref]
  • [24] A. Y. Koyfman, S. N. Magonov, N. O. Reich, Langmuir 25, 1091 (2009) http://dx.doi.org/10.1021/la801306j[Crossref]
  • [25] D. H. Mengistu, K. Bohinc, S. May, J. Phys. Chem. B 113, 12277 (2009) http://dx.doi.org/10.1021/jp904986j[Crossref]
  • [26] Z. Li, Y. Chen, X. Li, T. I. Kamins, K. Nauka, R. S. Williams, Nano Lett. 4, 245 (2004) http://dx.doi.org/10.1021/nl034958e[Crossref]
  • [27] Y. P. Ho, M. C. Kung, S. Yang, T. H. Wang, Nano Lett. 5, 1693 (2005) http://dx.doi.org/10.1021/nl050888v[Crossref]
  • [28] L. C. Brousseau, J. Am. Chem. Soc. 128, 11346 (2006) http://dx.doi.org/10.1021/ja063022f[Crossref]
  • [29] C. N. LaFratta, D. R. Walt, Chem. Rev. 108, 614 (2008) http://dx.doi.org/10.1021/cr0681142[Crossref]
  • [30] K. Tawa, W. Knoll, Nucleic Acids Res. 32, 2372 (2004) http://dx.doi.org/10.1093/nar/gkh572[Crossref]
  • [31] J. B. Fiche, A. Buhot, R. Calemczuk, T. Livache, Biophys. J. 92, 935 (2007) http://dx.doi.org/10.1529/biophysj.106.097790[Crossref]
  • [32] A. Gunnarsson, P. Jönsson, R. Marie, J. O. Tegenfeldt, F. Höök, Nano Lett. 8, 183 (2008) http://dx.doi.org/10.1021/nl072401j[Crossref]
  • [33] A. Gunnarsson, P. Jönsson, V. P. Zhdanov, F. Höök, Nucleic Acids Res. 37, e99 (2009) http://dx.doi.org/10.1093/nar/gkp487[Crossref]
  • [34] A. Sassolas, B. D. Leca-Bouvier, L. J. Blum, Chem. Rev. 108, 109 (2008) http://dx.doi.org/10.1021/cr0684467[Crossref]
  • [35] E. E. Nikitin, Theory of Elementary Atomic and Molecular Processes in Gases (Clarendon, Oxford, 1974)
  • [36] J. Svitel, H. Boukari, D. Van Ryk, R. C. Willson, P. Schuck, Biophys. J. 92, 1742 (2007) http://dx.doi.org/10.1529/biophysj.106.094615[Crossref]
  • [37] S. Pasche, M. Textor, L. Meagher, N. D. Spencer, H. J. Griesser, Langmuir 21, 6508 (2005) http://dx.doi.org/10.1021/la050386x[Crossref]
  • [38] V. Castells, S. X. Yang, P. R. Van Tassel, Phys. Rev. E 65, 031912 (2002) http://dx.doi.org/10.1103/PhysRevE.65.031912[Crossref]
  • [39] B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter, Molecular Biology of the Cell (Garland, New York, 2002)
  • [40] A. -L. Barabasi, H. E. Stanley, Fractal Concepts in Surface Growth (Cambridge University Press: Cambridge, 1995)
  • [41] K. Binder, In: K. Binder (Ed.), Monte Carlo Methods in Statistical Physics (Springer: Berlin, 1979) 1
  • [42] S. A. Rice, Diffusion-Limited Reactions (Elsevier: Amsterdam, 1985)
  • [43] H. Kim, K. J. Shin, Phys. Rev. Lett. 82, 1578 (1999) http://dx.doi.org/10.1103/PhysRevLett.82.1578[Crossref]
  • [44] H. Kim, K. J. Shin, J. Phys.-Condens. Mat. 19, 065137 (2007) http://dx.doi.org/10.1088/0953-8984/19/6/065137[Crossref]
  • [45] S. Park, N. Agmon, J. Phys. Chem. B 112, 12104 (2008) http://dx.doi.org/10.1021/jp803873p[Crossref]
  • [46] W. Min, X. S. Xie, B. Bagchi, J. Chem. Phys. 131, 065104 (2009) http://dx.doi.org/10.1063/1.3207274[Crossref]

Document Type

Publication order reference

Identifiers

YADDA identifier

bwmeta1.element.-psjd-doi-10_2478_s11534-010-0012-1
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.