Super-coiling

All of the steps from the unwinding of the original DNA double helix to the super coiling of the new DNAs are catalyzed by enzymes... 

The structure of the nucleosome is affected by ionic environment. The low ion concentration makes a nucleosomal array well spread whereas 100 mM NaCl induces nucleosome-nucleosome interaction (Hizume et al, 2005 Nakai et al, 2005 Olins and Olins, 1972 Thoma et al, 1979). In vitro transcription system has been applied to understand the relationship between the nucleosome assembly and transcription activity. The results demonstrated that a positive super-coiling introduced during the progress of RNA polymerase makes the nucleosomes ahead of the polymerase unstable (Pfaffle et al, 1990). 

The weakly immunogenic protamine sulfate USP (1) condenses DNA to form a toroid structure of super-coiled DNA about 50 nm in diameter (2). The DNA in this form or in the preformed LPDI complex cannot be displaced from the protamine by polycations such as spermidine and histones or by other nucleic acids like genomic DNA (2). DNA in this toroid structure is transcriptionally inactive and this conformation allows for protection of DNA from enzymatic degradation by nucleases and other environmental assaults such as mechanical stress (1,2). After the liposome surrounds the toroid, the resulting homogenous LPDI nanoparticles are slightly less than... 

Cellular DNA, as we have seen, is extremely compacted, implying a high degree of structural organization. The folding mechanism must not only pack the DNA but also permit access to the information in the DNA. Before considering how this is accomplished in processes such as replication and transcription, we need to examine an important property of DNA structure known as super-coiling. 

FIGURE 24-10 Supercoils. A typical phone cord is coiled like a DNA helix, and the coiled cord can itself coil in a supercoil. The illustration is especially appropriate because an examination of phone cords helped lead Jerome Vinograd and his colleagues to the insight that many properties of small circular DNAs can be explained by super-coiling. They first detected DNA supercoiling, in small circular viral DNAs, in 1965. 

That DNA would bend on itself and become super-coiled in tightly packaged cellular DNA would seem logical, then, and perhaps even trivial, were it not for one additional fact many circular DNA molecules remain highly supercoiled even after they are extracted and purified, freed from protein and other cellular components. This indicates that supercoiling is an intrinsic property of DNA tertiary structure. It occurs in all cellular DNAs and is highly regulated by each cell. 

HGURE 24-35 Model for the effect of condensins on DNA super-coiling. Binding of condensins to a closed-circular DNA in the presence of topoisomerase I leads to the production of positive supercoils (+). Wrapping of the DNA about the condensin introduces positive supercoils because it wraps in the opposite sense to a solenoidal supercoil (see Fig. 24-24).The compensating negative supercoils (—) that appear elsewhere in the DNA are then relaxed by topoisomerase I. In the chromosome, it is the wrapping of the DNA about condensin that may contribute to DNA condensation. 

During replication of DNA (Chapter 27) pairing of some bases associated with the replication apparatus is prevented. Upon release of the constraint the newly replicated DNA forms base pairs and becomes super-coiled. 

Until rather recently there had been little to indicate that DNA actually assumes cruciform conformations in cells. However, strong experimental evidence suggests that some cruciform structures do form naturally.380 Their formation from palindromic DNA [like the formation of Z-DNA from (G + C)-rich sequences] is a way of relieving torsional strain induced by super-coiling. Whether or not cruciform structures occur frequently within cells, there is no doubt that palindromic sequences are of great importance in the interaction of nucleic acids with symmetric dimeric and tetrameric protein molecules such as the gene repressor protein shown in Fig. 5-35.381-383... 

Most functions of DNA and RNA are dependent on proteins. Cells contain a vast array of polypeptides that bind to nucleic acids in many specific ways.387 390 We have seen (Fig. 5-21) that the histones hold super-coiled DNA in the form of nucleosomes391 in eukaryotic nuclei and similar proteins bind to and protect the... 

Figure 27-29 Formation of a synaptic complex of a super-coiled circular DNA containing the sites gix (green), which pass over and under the enhancer (gray). The recombinase Gin and the enhancer-binding Fis form a synaptic complex with DNA in this form as seen directly by electron microscopy. From Sadowski.576...

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