Abstract:
A typical B-DNA molecule, which is a right handed helix, consists of two complementary
polynucleotide chains that intertwine periodically to form a double helical structure. This
provides topological features of the DNA structure. Moreover, nucleic acids undergo
transactions in major cellular processes during replication, repair and transcription for which
accessibility of various factors to DNA is required. Thus, for commencement of several cellular
processes, melting of the duplex DNA structure is necessary. For all natural DNA molecules,
free end rotations can either be restricted or forbidden that can lead to DNA being overwound or
underwound (Mirkin 2001). When a DNA segment is constrained such that the free rotation of
its ends is prohibited, it forms a region known as a topological domain. The classical example of
a topological domain is a bacterial chromosome which is a covalently closed circular DNA
molecule, the nucleiod. Eukaryotic chromosomes consisting of linear DNAs also contain
topological domains in the form of DNA molecules in between two protein bodies. There are
certain features of topologically constrained DNA molecules that make them advantageous in the
course of natural selection. If a local change in the DNA structure can be sensed globally,
integrity of a DNA molecule can be ensured. In eukaryotes, supercoils are accumulated in
chromatin, where DNA is packaged into histones to be chromatinised. Supercoiling ensures that
DNA is not broken or damaged. Hence, altered topological states of DNA in a cell ensure proper
functioning of most physiological processes. To circumvent topology complications, each cell
employs a class of nucleic acid remodeling enzymes called topoisomerases(Mirkin 2001, Witz
and Stasiak 2010).
