Two-dimensional (2D) agarose gel electrophoresis is one of the most powerful methods to analyze the mass and shape of replication intermediates. It is often use to map replication origins but it is also useful to characterize termination of replication, replication fork barriers and even replication fork reversal. Here, we present protocols, figures and… (More)
Fig. 7. Replication fork stalling: (A) Mixture of DNA fragments containing replication forks that move from left to right unconstrained or stall at specific sites called replication fork barriers (RFBs). All the RIs are simple-Ys but those containing forks stalled at specific sites are more abundant. (B) 2D gel pattern generated by a population of RIs all replicated by a single fork that moves from one end to the other of the fragment. In some RIs, however, the replication fork stalls at a specific site and as a consequence these RIs containing a fork stalled at a specific site are more abundant in the population and generate a stronger signal (see Supplementary Videos 21 and 22).