Tuesday, April 8, 2008

DNA supercoil

In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10.4 base pairs of sequence. Adding or subtracting twists, as some enzymes can do, imposes strain. If a DNA segment under twist strain were to be closed into a circle by joining its two ends and then it is allowed to move freely, the circular DNA would contort into new shape, such as a simple figure-eight. Such a contortion is a supercoil.

The simple figure eight is the simplest supercoil, and is the shape a circular DNA assumes to accommodate one too many or one too few helical twists. The two lobes of the figure eight will appear rotated either clockwise or counterclockwise with respect to one another, depending on whether the helix is over or underwound. For each additional helical twist being accommodated, the lobes will show one more rotation about their axis.

The noun form "supercoil" is rarely used in the context of DNA topology. Instead, global contortions of a circular DNA, such as the rotation of the figure-eight lobes above, are referred to as writhe. The above example illustrates that twist and writhe are interconvertible. "Supercoiling" is an abstract mathematical property, and represents the sum of twist and writhe. The twist is the number of helical turns in the DNA and the writhe is the number of times the double helix crosses over on itself (these are the supercoils). The relationship of twist, writhe and supercoiling is expressed as the equation:

S = T + W.

Extra helical twists are positive and lead to positive supercoiling, while subtractive twisting causes negative supercoiling. Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology. DNA of most organisms is negatively supercoiled.

In part because chromosomes may be very large, segments in the middle may act as if their ends are anchored. As a result, they may be unable to distribute excess twist to the rest of the chromosome or to absorb twist to recover from underwinding--the segments may become supercoiled, in other words. In response to supercoiling, they will assume an amount of writhe, just as if their ends were joined.

Supercoiled DNA forms two structures; a plectoneme or a toroid, or a combination of both. A negatively supercoiled DNA molecule will produce either a one-start left-handed helix, the toroid, or a two-start right-handed helix with terminal loops, the plectoneme. Plectonemes are typically more common in nature, and this is the shape most bacterial plasmids will take. For larger molecules it is common for hybrid structures to form - a loop on a toroid can extend into a plectoneme. If all the loops on a toroid extend then it becomes a branch point in the plectonemic structure.

Image:Circular DNA Supercoiling.png
Size of this preview: 392 × 599 pixels

Supercoiled structure of circular DNA molecules with low writhe. Note that the helical nature of the DNA duplex is omitted for clarity.

Image:Linear DNA Supercoiling.png
Size of this preview: 800 × 474 pixels

Supercoiled structure of linear DNA molecules with constrained ends. Note that the helical nature of the DNA duplex is omitted for clarity


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