Topological aspects of DNA structure arise primarily from the fact that the two DNA strands are repeatedly intertwined. Untangling these two strands, which occurs in all major genetic processes may prove rather difficult. In the simplest case of a linear DNA in solution, untangling is possible due to the free rotation of the ends of the DNA. However, for all natural DNAs, free end rotation is either restricted or forbidden altogether. Consequently, untangling the two DNA strands becomes topologically impossible (Figure 1 illustrates this for the imaginary case of a circular DNA molecule where the two strands are tangled only once).
A DNA segment constrained so that the free rotation of its ends is impossible is called a topological domain (Figure 2). A canonical example of a topological domain is circular DNA, which is typical of bacteria, mitochondria, chloroplasts, many viruses, etc. In this case, there are obviously no DNA ends at all, since both DNA strands are covalently closed. Although eukaryotic chromosomes are linear overall, they consist of large DNA loops firmly attached to the nuclear matrix. These loops represent topological domains, i.e. they are equivalent to circular DNA topologically. The ends of linear DNA can also be affixed to the membrane, as has been shown for some viruses, making this DNA topologically closed. Finally, a stretch of DNA situated between the two massive protein bodies can also be considered a topological domain.
Source : DNA Topology Fundamentals