Defects and DNA Replication

We introduce a rate-equation formalism to study DNA replication kinetics in the presence of defects resulting from DNA damage and find a crossover between two regimes: a normal regime, where the influence of defects is local, and an initiation-limited regime. In the latter, defects have a global impact on replication, whose progress is set by the rate at which origins of replication are activated, or initiated. Normal, healthy cells have defect densities in the normal regime. Our model can explain an observed correlation between interorigin separation and rate of DNA replication.

Figure 1

Space-time diagram of replication. (a) During normal replication, the point $x$ is replicated at time $\le t$ only if a fork is activated within the shaded triangular area. (b), (c) Fork blocks (defects) near $x$ can reduce the relevant space-time area and thereby delay replication at $x$. (b) For small $\tau$, forks can initiate to the left of the defect ($x<x_d$), stall for a time $\tau$, and still replicate $x$ before $t$. (c) For large $\tau$, forks to the left of the defect cannot replicate $x$ before $t$.

Figure 2

(a) Replication fraction $f_0(t)$ for a section of an infinite genome ($v={10}^{-2}\mathrm{kb}/\sec$ and $I=5\times {10}^{-4}{\mathrm{kb}}^{-1}{\sec }^{-1}$ [29]). (b) Replication fraction $f(x,t)$ with a defect at $x=x_d$ and an infinite repair time ($\tau \to \infty$). (c) $\Delta f=f_0-f$. The defect influences the replication kinetics in the space-time area above the $\mathsf{V}$-shaped line ($vt=|x-x_d|$).

Figure 3

Interorigin distance vs defect density for $\tau \to \infty$. The solid gray line is the numerical solution to the scaled REs. Symbols indicate estimates from Table .

Figure 4

Interorigin distance vs effective velocity. The two solid lines are the numerical solutions to the scaled REs when $\tau /t_0\to 0$ and $\tau /t_0\to \infty$. Symbols correspond to measurements on different human cells.