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Mechanistic Insight into the Structure and Dynamics of Entangled and Hydrated λ-Phage DNA

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journal contribution
posted on 03.05.2012, 00:00 by Sandipan Chakraborty, Takashi Uematsu, Christer Svanberg, Per Jacobsson, Jan Swenson, Michael Zäch, Rajendar Trehan, George Armstrong, Bidisha Sengupta
Intrinsic dynamics of DNA plays a crucial role in DNA–protein interactions and has been emphasized as a possible key component for in vivo chromatin organization. We have prepared an entangled DNA microtube above the overlap concentration by exploiting the complementary cohesive ends of λ-phage DNA, which is confirmed by atomic force microscopy and agarose gel electrophoresis. Photon correlation spectroscopy further confirmed that the entangled solutions are found to exhibit the classical hydrodynamics of a single chain segment on length scales smaller than the hydrodynamic length scale of single λ-phage DNA molecule. We also observed that in 41.6% (gm water/gm DNA) hydrated state, λ-phage DNA exhibits a dynamic transition temperature (Tdt) at 187 K and a crossover temperature (Tc) at 246 K. Computational insight reveals that the observed structure and dynamics of entangled λ-phage DNA are distinctively different from the behavior of the corresponding unentangled DNA with open cohesive ends, which is reminiscent with our experimental observation.