The non-homologous end-joining (NHEJ) pathway for the repair of DNA double-strand breaks: I. A mathematical model.

This article presents a biochemical kinetic model for the non-homologous end joining (NHEJ) of DNA double-strand break (DSB) repair pathway. The model is part of a theoretical framework to encompass all cellular DSB repair pathways. The NHEJ model was developed by taking into consideration the biological characteristics of the repair processes in the absence of homologous recombination (HR), the major alternative pathway for DSB repair. The model considers fast and slow components of the repair kinetics resulting in a set of differential equations that were solved numerically. In the absence of available published data for reaction rate constants for the repair proteins involved in NHEJ, we propose reaction rate constants for the solution of the equations. We assume as a first approximation that the reaction rate constants are applicable to mammalian cells under same conditions. The model was tested by comparing measured and simulated DSB repair kinetics obtained with HR-deficient cell lines irradiated by X rays in the dose range of 20-80 Gy. Measured data for initial protein recruitment to a DSB were used to independently estimate rate constants for Ku70/Ku80 and DNA-dependent protein kinase catalytic subunit (DNA-PKcs). We show here based on the model of DSB repair described in this article, application of the model in the accompanying article (Taleei et al., Radiat. Res. 179, 540-548, 2013) and by simulation of repair times for each individual DSB produced by individual tracks of electrons, that the complexity of damage may explain the slow kinetics of DNA DSB repair.