DNA supercoil

DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand. Supercoiling is important in a number of biological processes, such as compacting DNA, and by regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism and possibly gene expression. Additionally, certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions such as DNA replication or transcription. Mathematical expressions are used to describe supercoiling by comparing different coiled states to relaxed B-form DNA.In a 'relaxed' double-helical segment of B-DNA, the two strands twist around the helical axis once every 10.4–10.5 base pairs of sequence. Adding or subtracting twists, as some enzymes can do, imposes strain. If a DNA segment under twist strain were closed into a circle by joining its two ends and then allowed to move freely, the circular DNA would contort into a new shape, such as a simple figure-eight. Such a contortion is a supercoil. The noun form 'supercoil' is often used in the context of DNA topology.Based on the properties of intercalating molecules i.e., fluorescing upon binding to DNA and unwinding of DNA base-pairs, recently a single-molecule technique has been introduced to directly visualize individual plectonemes along supercoiled DNA which would further allow to study the interactions of DNA processing proteins with supercoiled DNA. In that study, Sytox Orange (an intercalating dye), has been used to induce supercoiling on surface tethered DNA molecules.DNA supercoiling is important for DNA packaging within all cells. Because the length of DNA can be thousands of times that of a cell, packaging this genetic material into the cell or nucleus (in eukaryotes) is a difficult feat. Supercoiling of DNA reduces the space and allows for DNA to be packaged. In prokaryotes, plectonemic supercoils are predominant, because of the circular chromosome and relatively small amount of genetic material. In eukaryotes, DNA supercoiling exists on many levels of both plectonemic and solenoidal supercoils, with the solenoidal supercoiling proving most effective in compacting the DNA. Solenoidal supercoiling is achieved with histones to form a 10 nm fiber. This fiber is further coiled into a 30 nm fiber, and further coiled upon itself numerous times more.In nature, circular DNA is always isolated as a higher-order helix-upon-a-helix, known as a superhelix. In discussions of this subject, the Watson-Crick twist is referred to as a 'secondary' winding, and the superhelices as a 'tertiary' winding. The sketch at right indicates a 'relaxed', or 'open circular' Watson-Crick double-helix, and, next to it, a right-handed superhelix. The 'relaxed' structure on the left is not found unless the chromosome is nicked; the superhelix is the form usually found in nature.The topological properties of circular DNA are complex. In standard texts, these properties are invariably explained in terms of a helical model for DNA, but in 2008 it was noted that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations.