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DNA gyrase, or simply gyrase, is an enzyme within the class of topoisomerase and is a subclass of Type II topoisomerases [1] that reduces topological strain in an ATP dependent manner while double-stranded DNA is being unwound by elongating RNA-polymerase [2] or by helicase in front of the progressing replication fork.
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 diagram shows the effects of nicks on intersecting DNA in a twisted plasmid. Nicking can be used to dissipate the energy held up by intersecting states. The nicks allow the DNA to take on a circular shape. [2] The diagram shows the effects of nicks on intersecting DNA forms. A plasmid is tightly wound into a negative supercoil (a).
Based on the properties of intercalating molecules, i.e. fluorescing upon binding to DNA and unwinding of DNA base-pairs, in 2016, a single-molecule technique has been introduced to directly visualize individual plectonemes along supercoiled DNA [5] which would further allow to study the interactions of DNA processing proteins with supercoiled DNA.
DNA in cells is negatively supercoiled and has the tendency to unwind. Hence the separation of strands is easier in negatively supercoiled DNA than in relaxed DNA. The two components of supercoiled DNA are solenoid and plectonemic. The plectonemic supercoil is found in prokaryotes, while the solenoidal supercoiling is mostly seen in eukaryotes.
The packaging of eukaryotic DNA into chromatin is a barrier to all DNA-based processes that require enzyme action. For most DNA repair processes, the chromatin must be remodeled . In eukaryotes, ATP -dependent chromatin remodeling complexes and histone-modifying enzymes are two factors that act to accomplish this remodeling process after DNA ...
One example of a Z-DNA binding protein is the vaccinia E3L protein, which is a product of the E3L gene and mimics a mammalian protein that binds Z-DNA. [37] [38] Not only does the E3L protein have affinity to Z-DNA, it has also been found to play a role in the level of severity of virulence in mice caused by vaccinia virus, a type of poxvirus.
Cruciform DNA is found in both prokaryotes and eukaryotes and has a role in DNA transcription and DNA replication, double strand repair, DNA translocation and recombination. They also serve a function in epigenetic regulation along with biological implications such as DNA supercoiling, double strand breaks, and targets for cruciform-binding ...