21] Dynamic light scattering for study of solution conformation and dynamics of superhelical DNA

Abstract

Dynamic light scattering is a powerful tool for studying the shape and internal motions of flexible biopolymers, such as DNA. For superhelical DNA at small scattering angles, the rigid rod model can be applied with good success to obtain the translational and rotational diffusion coefficients of the molecule. The result from the model leads to the conclusion that superhelical DNA molecules in solution have an elongated, interwound structure. This structure shows a high degree of internal motion that can be described by segmental diffusion with a diffusion coefficient corresponding to the independent motion of DNA pieces that are 300 base pairs (bp) long. The overall elongated shape of the DNA is determined by the topological constraints arising from the circularity and internal torsional stress. A practical consequence of this model is that a time can be estimated that characterizes the mutual diffusion of distant parts of the DNA. In a 10,000 bp superhelical DNA, one piece of the DNA needs about 0.4 msec to move from one end of the structure to the other.