Persistence Length of DNA Macromolecule with Kinks

The study of configurational parameters of deformed DNA is a relevant problem in research of such important biological process as double helix compactization in cell. The deformations accompanied with local disruptions of the regular macromolecule structure cause significant bending of the double helix, or kinks. In this paper an approach for Kratky-Porod model to calculate persistence length of DNA macromolecule with kinks is developed. The presented approach considers kinks of arbitrary configuration, including two basic types of kinks, type 1 - sharp kink caused by unstacking a single base pair step, and type 2 - intrinsic-induced kink that involves several base pairs. Within developed approach analytical expressions for persistence length, coil size and gyration radius of kinky double helix were obtained.