Negative supercoiling of DNA

Topoisomerase I catalyzes the relaxation of negatively supercoiled DNA no coreactants are needed. Topoisomerase II catalyzes the negative supercoiling of DNA, using ATP as a coreactant, and it is also able to relax positive supercoiling (Chap. 7). 

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. 

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. 

Figure 10.28 Formation of negatively supercoiled circular DNA by gyrase. This type of DNA is present in bacterial chromosomes and plasmids. Positively supercoiled DNA has the opposite handedness.

Type I topoisomerases catalyze the relaxation of supercoiled DNA, a thermodynamically favorable process. Type II topoisomerases utilize free energy from ATP hydrolysis to add negative supercoils to DNA. The two types of enzymes have several common features, including the use of key tyrosine residues to form covalent links to the polynucleotide backbone that is transiently broken. 

The addition of AMP-PNP to topoisomerase II and circular DNA leads to the negative supercoiling of a single molecule of DNA per enzyme. DNA remains bound to the enzyme in the presence of this analog. What does this finding reveal about the catalytic mechanism ... 

The quinolones include nalidixic acid (NegGram), cinoxacin, norfloxacin (Noroxin), and ciprofloxacin (Cipro). Other members of the quinolone family are pefloxacin, ofloxacin, enoxacin, and fleroxacin. The bacterial DNA gyrase is responsible for the continuous introduction of negative supercoils into DNA, and the quinolones inhibit this gyrase-mediated DNA supercoiling (see Figure 85). 

The bacterial enzyme DNA gyrase is responsible for the continuous introduction of negative supercoils into DNA, and the quinolones inhibit this gyrase-mediated DNA super-coiling. 

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