Sometimes the DNA replication fork stalls as it can’t process damaged bases. Damaged bases must be replaced for replication to continue.
DNA is being constantly damaged by factors both inside and outside of the cell. DNA can be damaged in lots of different ways. One example of DNA damage is inter-strand crosslinks (ICLs), where the two opposite strands of the DNA become chemically linked together.
Damaged DNA, such as ICLs, can cause DNA replication forks to stall. When the replication fork reaches the DNA it stops because it can’t process damaged bases. The DNA damage needs to be repaired in order for the replication of the DNA to continue. In the case of ICLs, the damaged bases are cut out by enzymes called nucleases. The bases are then replaced in order to allow replication to continue.