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Illustration of how cold shock affects the supercoiling state of the DNA, by blocking the activity of Gyrase. The signs ' − ' and '+' represent negative and positive supercoiling, respectively. Created with BioRender.com. Also shown is a stochastic model of gene expression during cold shock as a function of the global DNA supercoiling state.
Negative supercoiling, also referred to as underwinding, results in the counterclockwise twisting of the DNA strand. Negative supercoiling leaves the DNA strands available for various cellular processes, like genome replication and transcription, as DNA typically needs to be underwound in order to be denatured and accessed by the proper enzymes ...
DNA gyrase is a tetrameric enzyme that consists of 2 GyrA ("A") and 2 GyrB ("B") subunits. [8] Structurally the complex is formed by 3 pairs of "gates", sequential opening and closing of which results into the direct transfer of DNA segment and introduction of 2 negative supercoils. N-gates are formed by ATPase domains of GyrB subunits.
Precatenanes form as the newly-synthesised duplexes wrap around one and other, and, if not removed prior to complete of replication, catenated DNA molecules are formed. ii) During transcription, strand separation leads to positive supercoiling ahead of the advancing protein machinery, and negative supercoil formation behind. [1]
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.
The enzyme uses the hydrolysis of ATP to introduce positive supercoils and overwinds DNA, a feature attractive in hyperthermophiles, in which reverse gyrase is known to exist. Rodriguez and Stock have done further work to identify a "latch" that is involved in communicating the hydrolysis of ATP to the introduction of positive supercoils.
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.
While topoisomerase IV does relax positive supercoils like DNA gyrase, it does not introduce further negative supercoiling like the latter enzyme. [ 1 ] Topoisomerase IV can unknot right-handed knots and decatenate right-handed catenanes without acting on right-handed plectonemes in negatively supercoiled DNA molecules, based on geometrical ...