Positively supercoiled DNA

Positively supercoiled DNA is formed if the DNA is wound more tightly than in Watson-Crick DNA. 

Hamiche, A., Carol, V., Alilat, M., De Lucia, F., O Donohue, M.F., Revet, B., and Prunell, A. (1996) Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles. Potential flipping of the protein from a left- to a right-handed superhelical form. PNAS (USA) 93, 7588-7593. 

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.

A type II DNA topoisomerase has been detected by Kikuchi and coworkers in S. acidocaldarius [95]. This enzyme seems to be much less abundant and active than reverse gyrase. It exhibits the usual ATP requirement of type II DNA topoisomerases (in the millimolar range) and can relax either negatively or positively supercoiled DNA. 

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-... 

ATP may stimulate or inhibit DNA relaxation by some eucaryotic type I enzymes. Will relax positively supercoiled DNA only in the presence of ADPNP. 

Among the two types of topoisomerases, some enzymes are able to carry out only a subset of the reactions shown in Figs. 2 and 3. For example, the type I topoisomerase from mouse embryo is able to relax positively supercoiled DNA (Champoux and Dulbecco, 1972), whereas... 

Cleavage occurs four nucleotides from the 5 end and three nucleotides from the 3 end. The enzyme binds to a negatively supercoiled DNA and does not form a complex with relaxed or positively supercoiled DNA. Eukaryotic type I (IB) topoisomerase binds dsDNA covering a region of 20bp. The enzyme is able to ranove both negative and positive supercoils. 

Rg. 2. Main reaction catalyzed by reverse gytases ATP-dependent Unking number increase. Sup negatively supercoiled DNA (right-handed superhelix), equivalent to an underwinding of the double helix Sup positively supercoiled DNA (left-handed superhelix), equivalent to a overwinding of the double helix. 

Figure 3 shows the disappearance of the form I DNA substrate (Fig. 3a) and the appearence of positively supercoiled DNA that forms the right part of the arch (Fig. 3c). In processive conditions, i.e., low ionic strength (30 mM NaCl), and in the presence of higher enzyme concentrations or of condensing agents, efficient positive supercoiling (superhelical density o > -1-0.05) is obtained (Fig. 3d). By contrast, in the absence of ATP, an inefficient DNA relaxation occurs, but there is no positive supercoiling (Fig. 3b).

The unique enzymatic activity of reverses gyrases, i.e., the efficient production of positively supercoiled DNA, was used by a number of authors to estimate the impact of such a DNA structure on various biological mechanisms. These include chromatin stability,recombination, and transcription. However, the in vivo role of reverse gyrases in hyperthermophiles remains a matter of speculation. It was suggested long ago that one of the main functions of topoisomerases is to tightly... 

The main structural difference between DNA gyrase and the other Topo IIA enzymes resides in the C-terminal region of GyrA, which appears to be essential for the wrapping of the DNA around enzyme. Indeed, removal of this C-terminal region transforms DNA gyrase into a classical Topo II that can only relax either negatively or positively supercoiled DNA. ... 

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