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