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If a DNA segment under twist strain is closed into a circle by joining its two ends, and then allowed to move freely, it takes on different shape, such as a figure-eight. This shape is referred to as a supercoil. (The noun form "supercoil" is often used when describing DNA topology.) The DNA of most organisms is usually negatively supercoiled.
Contrary to intuition, a topological property, the linking number, arises from the geometric properties twist and writhe according to the following relationship: L k = T + W, where L k is the linking number, W is the writhe and T is the twist of the coil. The linking number refers to the number of times that one strand wraps around the other.
After introducing a nick in the system, the negative supercoil gradually unwinds (c) until it reaches its final, circular, plasmid state (d). [2] Nicked DNA can be the result of DNA damage or purposeful, regulated biomolecular reactions carried out in the cell. During processing, DNA can be nicked by physical shearing, over-drying, or enzymes.
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DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound. [43]
In DNA double helix, the two strands of DNA are held together by hydrogen bonds. The nucleotides on one strand base pairs with the nucleotide on the other strand. The secondary structure is responsible for the shape that the nucleic acid assumes. The bases in the DNA are classified as purines and pyrimidines. The purines are adenine and guanine ...
Type II topoisomerases increase or decrease the linking number of a DNA loop by 2 units, and it promotes chromosome disentanglement. For example, DNA gyrase, a type II topoisomerase observed in E. coli and most other prokaryotes, introduces negative supercoils and decreases the linking number by 2.
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