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Physical Review E

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Enhanced bubble formation in looped short double-stranded DNA

O-chul Lee^* and Wokyung Sung^†

Department of Physics and PCTP, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea

^*ochul_lee@postech.ac.kr
^†wsung@postech.ac.kr

Phys. Rev. E 85, 021902 – Published 3 February, 2012

DOI: https://doi.org/10.1103/PhysRevE.85.021902

Abstract

Recent experiments have shown the double-stranded (ds) DNAs readily bend and loop over the scale much shorter than their persistence length (50 nm). In an effort to unveil this seemingly surprising phenomenon, we study the emergence of bubbles in short ds DNA loops by simulating the breathing DNA model. We analyze the bubble size distributions and the melting curves for varying contour lengths, which are critically compared with those of linear DNA of the same lengths. We analytically evaluate the free energies associated with double-strand bending and single-strand bubble formation to explain the simulation data. It is found that in shorter looped DNA the bubbles are more easily initiated and formed to release the large bending energy, giving rise to melting at a lower temperature and a lower contour length.

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References (24)

E. T. Kool, Annu. Rev. Biophys. Biomol. Struct. 30, 1 (2001).
B. Tinland, A. Pluen, J. Sturm, and G. Weill, Macromolecules 30, 5763 (1997); M. D. Wang, H. Yin, R. Landick, J. Gelles, and S. M. Block, Biophys. J. 72, 1335 (1997).
T. E. Cloutier and J. Widom, Mol. Cell 14, 355 (2004).
Q. Du, C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. Vologodskii, Proc. Natl. Acad. Sci. USA 102, 5397 (2005).
R. A. Forties, R. Bundschuh, and M. G. Poirier, Nucleic Acids Res. 37, 14 (2009).
J. Yan and J. F. Marko, Phys. Rev. Lett. 93, 108108 (2004).
P. A. Wiggins, R. Phillips, and P. C. Nelson, Phys. Rev. E 71, 021909 (2005).
J. Yan, R. Kawamura, and J. F. Marko, Phys. Rev. E 71, 061905 (2005).
F. H. C. Crick and A. Klug, Nature (London) 255, 530 (1975).
J. S. Mitchell, C. A. Laughton, and S. A. Harris, Nucleic Acids Res. 39, 3928 (2011).
A. Wildes, N. Theodorakopoulos, J. Valle-Orero, S. Cuesta-Lopez, J.-L. Garden, and M. Peyrard, Phys. Rev. Lett. 106, 048101 (2011).
J.-H. Jeon and W. Sung, Biophys. J. 95, 3600 (2008).
O-chul Lee, J. H. Jeon, and W. Sung, Phys. Rev. E 81, 021906 (2010).
J.-Y. Kim, J.-H. Jeon, and W. Sung, J. Chem. Phys. 128, 055101 (2008).
J. Jeon, W. Sung, and F. H. Ree, J. Chem. Phys. 124, 164905 (2006).
C. Yuan, H. Chen, X. W. Lou, and L. A. Archer, Phys. Rev. Lett. 100, 018102 (2008).
S. Cocco, R. Monasson, and J. F. Marko, Phys. Rev. E 65, 041907 (2002).
T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette, Biophys. J. 74, 2016 (1998).
V. Ivanov, Y. Zeng, and G. Zocchi, Phys. Rev. E 70, 051907 (2004).
V. Ivanov, D. Piontkovski, and G. Zocchi, Phys. Rev. E 71, 041909 (2005).
Y. Zeng, A. Montrichok, and G. Zocchi, J. Mol. Biol. 339, 67 (2004).
N. Douarche and S. Cocco, Phys. Rev. E 72, 061902 (2005).
P. J. Flory, Principles of Polymer Chemistry (Cornell University Press, Ithaca, 1971).
F. Brochard-Wyart, A. Buguin, and P. G. de Gennes, Europhys. Lett. 47, 171 (1999).