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

Journal article, 2012

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 lambda-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 lambda-phage DNA molecule. We also observed that in 41.6% (gm water/gm DNA) hydrated state, lambda-phage DNA exhibits a dynamic transition temperature (T-dt) at 187 K and a crossover temperature (T-c) at 246 K. Computational insight reveals that the observed structure and dynamics of entangled lambda-phage DNA are distinctively different from the behavior of the corresponding unentangled DNA with open cohesive ends, which is reminiscent with our experimental observation.