DNA Supercoiling:- Most Cellular DNA Is Underwound
To understand supercoiling, we must first focus on the properties of small circular DNAs such as plasmids and small viral DNAs. When these DNAs have no breaks in either strand, they are referred to as closed-circular DNAs. If the DNA of a closed-circular molecule con forms closely to the B-form structure , with one turn of the double helix per 10.5 bp, the DNA is relaxed rather than supercoiled . Supercoiling results when DNA is subject to some form of structural strain. Purified closed-circular DNA is rarely relaxed, regardless of its biological origin. Furthermore, DNAs derived from a given cellular source have a characteristic degree of supercoiling. DNA structure is therefore strained in a manner that is regulated by the cell to induce the super coiling.
In almost every instance, the strain is a result of underwinding of the DNA double helix in the closed circle. In other words, the DNA has fewer helical turns than would be expected for the B-form structure. The effects of underwinding are summarized in Figure 1. An 84 bp segment of a circular DNA in the re laxed state would contain eight double-helical turns, or one for every 10.5 bp. If one of these turns were re moved, there would be (84 bp)/7 12.0 bp per turn, rather than the 10.5 found in B-DNA (Fig. 1b). This is a deviation from the most stable DNA form, and the molecule is thermodynamically strained as a result. Generally, much of this strain would be accommodated by coiling the axis of the DNA on itself to form a supercoil (Fig. 1c; some of the strain in this 84 bp segment would simply become dispersed in the untwisted structure of the larger DNA molecule). In principle, the strain could also be accommodated by separating the two DNA strands over a distance of about 10 bp (Fig. 1d). In isolated closed-circular DNA, strain introduced by underwinding is generally accommodated by supercoiling rather than strand separation, because coiling the axis of the DNA usually requires less energy than breaking the hydrogen bonds that stabilize paired bases. Note, however, that the underwinding of DNA in vivo makes it easier to separate DNA strands, giving access to the information they contain. Every cell actively underwinds its DNA with the aid of enzymatic processes (described below), and the resulting strained state represents a form of stored en ergy. Cells maintain DNA in an underwound state to facilitate its compaction by coiling. The underwinding of DNA is also important to enzymes of DNA metabolism that must bring about strand separation as part of their function. The underwound state can be maintained only if the DNA is a closed circle or if it is bound and stabilized by proteins so that the strands are not free to rotate about each other. If there is a break in one strand of an iso lated, protein-free circular DNA, free rotation at that point will cause the underwound DNA to revert spontaneously to the relaxed state. In a closed-circular DNA molecule, however, the number of helical turns cannot be changed without at least transiently breaking one of the DNA strands. The number of helical turns in a DNA molecule therefore provides a precise description of supercoiling.
FIGURE 1 Effects of DNA underwinding. (a) A segment of DNA within a closed-circular molecule, 84 bp long, in its relaxed form with eight helical turns. (b) Removal of one turn induces structural strain. (c) The strain is generally accommodated by formation of a supercoil. (d) DNA underwinding also makes the separation of strands somewhat easier. In principle, each turn of underwinding should facilitate strand separation over about 10 bp, as shown. However, the hydrogen bonded base pairs would generally preclude strand separation over such a short distance, and the effect becomes important only for longer DNAs and higher levels of DNA underwinding.
