Topological challenges to DNA replication: Conformations at the fork

The unwinding of the parental DNA duplex during replication causes a positi ve linking number difference, or superhelical strain, to build up around th e elongating replication fork. The branching at the fork and this strain br ing about different conformations from that of (-) supercoiled DNA that is not being replicated. The replicating DNA can form (+) precatenanes, in whi ch the daughter DNAs are intertwined, and (+) supercoils. Topoisomerases ha ve the essential role of relieving the superhelical strain by removing thes e structures. Stalled replication forks of molecules with a (f) superhelica l strain have the additional option of regressing, forming a four-way junct ion at the replication fork. This four-way junction can be acted on by reco mbination enzymes to restart replication, Replication and chromosome foldin g are made easier by topological domain barriers, which sequester the subst rates for topoisomerases into defined and concentrated regions. Domain barr iers also allow replicated DNA to be (-) supercoiled. We discuss the import ance of replicating DNA conformations and the roles of topoisomerases.