Chakraborty S, Uematsu T, Svanberg C, Jacobsson P, Swenson J, Zäch M, Trehan R, Armstrong G, Sengupta B. Mechanistic insight into the structure and dynamics of entangled and hydrated λ-phage DNA.
J Phys Chem A 2012;
116:4274-84. [PMID:
22515820 DOI:
10.1021/jp2108363]
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Abstract
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 (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 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.
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