Negative supercoils. DNA

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-... 

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. 

Type I and type II topoisomerases relax negatively supercoiled DNA in steps of one and steps of two, respectively. Type II topoisomerases can also add additional negative supercoils (as indicated by the double arrow). The latter reaction requires energy input, which is encoded by ATP cleavage. 

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). 

From analyses of these structures and the results of other studies, the relaxation of negatively supercoiled DNA... 

In 1984, Kikuchi and Asai[72] discovered that partially purified protein fractions of S. acidocaldarius transform negatively supercoiled DNA into a positively supercoiled... 

An ATP-independent DNA topoisomerase activity has also been described in crude extracts of archaebacteria lacking reverse gyrase activity [91] (Fig. 7) and has been partially purified from T. acidophilum [90]. This enzyme specifically relaxes negatively supercoiled DNA and could be phylogenetically related either to reverse gyrase and/or to the DNA topoisomerase III of D. amylolyticus. 

Fig. 9. Positive supercoiling of SSVl DNA. Panels A and B show two-dimensional agarose gel electrophoresis of SSVl DNA isolated from cells of Sulfolobus shibatae, (A) before and (B) after UV induction (for methods see refs. [39,98]). The left-hand branch of the arch visible in A corresponds to negatively supercoiled DNA, the top of the arch corresponds to relaxed DNA and the right-hand branch corresponds to positively supercoiled DNA. The upper bands in A and B correspond to form II (open circular) and the middle band in B corresponds to form III (linear SSVl) (pictures courtesy of G. Mirambeau). Panel C shows a one-dimensional agarose gel electrophoresis of SSVl DNA isolated...

The first activity of DNA topoisomerases to be described was the relaxation of supercoiled closed-circular DNA, i.e., conversion to a less supercoiled form (Wang, 1971). This activity was clearly distinct from that of nucleases since the products were covalently closed and relaxation could occur in a stepwise fashion. A dependence on DNA ligase was ruled out, since no energy source was required for this reaction. All topoisomerases discovered subsequently can relax negatively supercoiled DNA the ability to relax positively supercoiled DNA is less gen-... 

Figure 2. Schematic representation of the unwinding of negatively supercoiled DNA caused by the binding of increasing amounts of drugs (dark circles). In the unwinding process, the topological linking number (a) remains invariant while the number of supercoils (t) changes. The DNA is shaded also to denote different...

Suppose that negatively supercoiled DNA with Lk = 23, Tw = 25, and Wr = -2 is acted on by topoisomerase 1. After one catalytic cycle, what would be the approximate values of Lk, Tw, and Wr ... 

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