Supercoils in closed DNA

The double helix structure of DNA represents a linear DNA molecule, but DNA in vivo often has a closed structure without any free ends. In bacteria and viruses, DNA is often circular. In eukaryotes also, large loops of DNA are found in such a way that each loop represents part of a circle. This organization puts an additional constraint on double helical structure, and the DNA becomes supercoiled (Fig. 25.19). One supercoil is introduced every time that the duplex thread is twisted about its axis. This supercoiling places a DNA molecule under torsion, which can be released by a break in one of the two strands. A DNA molecule without supercoiling is said to be relaxed.

The supercoils may be negative (as found in vivo), when they are in a direction opposite to the clockwise turns of right handed DNA. This will actually relieve the torsion and will become underwound or even single stranded in a region. This helps in unwinding of DNA for replication, etc. The positive supercoils lead to overwinding (superhelical), which can be created in vitro, but does not occur in nature. Supercoiling is often controlled by some enzymes and is described by parameters like linking number, twisting number and writhing number (for details, consult Lewin's 'Genes V').