Over winding vs under winding of a DNA

Question

DNA supercoiling refers to the over- or under-winding of a DNA strand.

Source : DNA supercoil

When a relaxed DNA is subjected to bends, or openings of DNA, over winding or unwinding, its base pairs per turn changes, and the DNA is subjected to stress and strain. In order to overcome such distortion, which has rendered the DNA unstable, the DNA twist around itself, like a circular rubber band undergoing twisting, such a twists on its own thread is called Super coiling; it is also referred to as tertiary structure.

Source : DNA Super Coiling

What they mean by over winding and under winding of a DNA ?

Answer 1

Imagine a covalently closed circular double-stranded DNA plasmid. In its "natural", or "relaxed" state you could spread it out, flat, on a suitable surface.

Now imagine cutting one of the strands of the DNA (i.e., cutting the sugar-phosphate backbone, the way that an endonuclease would, leaving a nick, the 5'-end of the nick has the phosphate, and the 3'-end of the nick has an -OH group), and rotating that nicked strand in a clockwise direction, several times, around the other, intact, DNA strand. This does not involve breaking any of the basepairs, or unravelling the strands, you are just twisting it around.

Now imagine sealing that nick, by ligating the 5' phosphate to the 3' OH. At this point the dsDNA helix is slightly "overwound", and will no long lie completely flat. It has begun to be supercoiled; these are positive supercoils.

If, alternatively, you had rotated the nicked DNA strand several turns in the counter-clockwise direction before re-sealing it then that molecule would also start to be supercoiled, but it would be "underwound" with negative supercoils (and it would also no longer lie flat on the surface).

There is an enzyme called DNA topoisomerase I that cuts, and re-seals, one of the two strands like this. Another enzyme called DNA topoisomerase II cuts both strands before introducing supercoils.

Answer 2

There are two types of supercoiling:

• Positive (right-handed/overwound) : the double helix is twisted to such an extent that it begins to ‘knot’.
• Negative (left-handed/underwound) : this type of coil goes against the natural direction of the double helix structure.

Negative supercoiling is a highly regulated process, performed by specific enzymes such as topoisomerases. There exist two types: topoisomerase I and topoisomerase II. The former relaxes the supercoil whereas the latter increases the extent to which the DNA is supercoiled.

In E. coli, there are at least four different types of topoisomerases responsible for regulating DNA supercoiling.

Source : SUPERCOILING