length effectively to about 4 nm. Indeed, our values of L eff p estimated from simulation with L$_{ss}$ (=4 nm) are in a good agreement with this experimental value. Simulating the Breathing DNA model that incorporates locally fluctuating persistence lengths depending upon the bp distances along the contour, we find that the distributions of bubbles and forks are nearly independent of the contour length, reducing the effective persistence length of the duplex for the short lengths. The forks dominate the bubbles in enhancing duplex flexibility and inducing unbinding transition. This work was supported by NCRC and BK 21. We thank L. A. Archer for a valuable communication. [1] D. L. Nelson and M. M. Cox, Lehninger Principles of Biochemistry , 3rd ed. (W. H. Freeman, New York, 2000); M. Gueron, M. Kochoyan and J. L. Leroy, Nature 328 , 89 (1987). [2] J. F. Marko and E. D. Siggia, Macromolecules 28 , 8759 (1995). [3] T. E. Cloutier and J. Widom, Molecular cell 14 , 355 (2004). [4] P. A. Wiggins et al. , Nature Nanotechnology 1 , 137 (2006). [5] C. Yuan, H. Chen, X. W. Lou, and L. A. Archer, Phys. Rev. Lett. 100 , 018102 (2008). [6] G. Altan-Bonnet, A. Libchaber, and O. Krichevsky, Phys. Rev. Lett. 90 , 138101 (2003). [7] J. Yan and J. F. Marko, Phys. Rev. Lett. 93 , 108108 (2004); P. Ranjith, P. B. Sunil Kumar, and G. I. Menon, Phys. Rev. Lett. 94 , 138102 (2005); H. Chen and J. Yan, Phys. Rev. E. 77 , 041907 (2008). [8] J.-Y. Kim, J.-H. Jeon, and W. Sung, J. Chem. Phys. 128 , 055101 (2008). [9] M. Peyrard and A. R. Bishop, Phys. Rev. Lett. 62 , 2755 (1989). [10] N. Theodorakopoulos, T. Dauxois, and M. Peyrard, Phys. Rev. Lett. 85 , 6 (2000). [11] J. B. Mills, E. Vacano, and P. J. Hagerman, J. Mol. Biol. 285 , 245 (1999); M. C. Murphy et al. , Biophys. J. 86 , 2530 (2004). [12] A similar description was also introduced in the Peyrard-Bishop-Dauxois model [10] where the stacking energy is described by a harmonic energy with a bp-distance dependent spring 10 Acknowledgments