Negative supercoiling

The native form of chromatin in cells assumes a higher order stmcture called the 30-nm filament, which adopts a solenoidal stmcture where the 10-nm filament is arranged in a left-handed cod (Fig. 5). The negative supercoiling of the DNA is manifested by writhing the hehcal axis around the nucleosomes. Chromatin stmcture is an example of toroidal winding whereas eukaryotic chromosomes are linear, the chromatin stmctures, attached to a nuclear matrix, define separate closed-circular topological domains. 

The difference between the linking number of a DNA and the linking number of its relaxed form is AL AL = (L — To) - In our example with four negative supercoils, AL = 4. The superhelix density or specific linking difference... 

Negatively supercoiled DNA can arrange into a toroidal state (Figure 12.26). The toroidal state of negatively supercoiled DNA is stabilized by wrapping around proteins which serve as spools for the DNA ribbon. This toroidal con-... 

Gyrase is another term for bacterial topoisomerase II. The enzyme consists of two A and two B subunits and is responsible for the negative supercoiling of the bacterial DNA. Negative supercoiling makes the bacterial DNA more compact and also more readily accessible to enzymes that cause duplication and transcription of the DNA to RNA. 

II ( gyrase ) II Tetramer (2 GyrA 2 GyrB subunits) gyrA/ gyrB Introduces negative supercoils into DNA... 

Bacterial as well as eukaryotic chromosomes contain too much DNA to fit easily into a cell. Therefore, the DNA must be condensed (compacted) to fit into the cell or nucleus. This is accomplished by supercoiling the DNA into a highly condensed form. When relaxed circular DNA is twisted in the direction that the helix turns, the DNA becomes positively supercoiled, if it is twisted in the opposite direction, it is called negatively supercoiled. Bacterial DNA is normally found in a negatively supercoiled state. Supercoiling reactions are catalyzed by topoisomerases. 

Negatively supercoiled DNA is formed if the DNA is wound more loosely than in Watson-Crick DNA. This form is required for most biologic reactions. 

Sheflin, L.G. and Spaulding, S.W. (1989) High mobility group protein 1 preferentially conserves torsion in negatively supercoiled DNA. Biochemistry 28, 5658-5664. 

Eukaryotic cells also have type I and type II topoisomerases. The type I enzymes are topoisomerases I and III the type II enzymes are topoisomerases Ha and II/3. The eukaryotic type II topoisomerases cannot underwind DNA (introduce negative supercoils), but they can relax both positive and negative supercoils. We consider one probable origin of negative supercoils in eukaryotic cells in our discussion of chromatin in Section 24.3. The process catalyzed by eukaryotic type II topoisomerases is illustrated in Figure 24-22. 

FIGURE 24-28 Chromatin assembly, (a) Relaxed, closed-circular DNA. (b) Binding of a histone core to form a nucleosome induces one negative supercoil, in the absence of any strand breaks, a positive supercoil must form elsewhere in the DNA (ALk = 0). (c) Relaxation of this positive supercoil by a topoisomerase leaves one net negative supercoil (ALk = -1). 

---