How dsDNA breathing enhances its flexibility and instability on short length scales PACS numbers: 87.14.gk, 87.15.A-, 87.15.hg University of Munich, James-Franck Strasse, Garching 85373, Germany $^{‡}$corresponding author:wsung@postech.ac.kr 1 arXiv:1001.1956v2 [cond-mat.soft] 13 Jan 2010 Abstract We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the duplex and also forks at the ends, with the size distributions independent of the contour length. We find that these local denaturations at a physiological temperature, despite their rare and transient presence, can lower the persistence length drastically for a short DNA segment in agreement with experiment. $^{∗}$Electronic address: lee572@postech.ac.kr $^{†}$Electronic address: jae-hyung.jeon@ph.tum.de; Present address: Physik Department (T30g), Technical O-chul Lee, ∗ Jae-Hyung Jeon, † and Wokyung Sung ‡ (Dated: October 30, 2018) Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea