Tertiary Structure of DNA Supercoils

Two questions arise in separating the two strands of the original DNA so that it can be replicated. The first is how to achieve continuous unwinding of the double helix. This question is complicated by the fact that prokaryotic DNA exists in a supercoiled, closed-circular form (see Tertiary Structure of DNA Supercoiling in Section 9.3). The second related question is how to protect single-stranded stretches of DNA that are exposed to intracellular nucleases as a result of the unwinding. 

A single helix is a coil a double helix is two nested coils The tertiary structure of DNA in a nucleosome is a coiled coil Coiled coils are referred to as supercoils and are quite common... 

The tertiary structure of DNA is complex. DNA does not normally exist as a straight linear polymer, but as a supercoiled structure. Supercoiiing is associated with special proteins in eukaryotic organisms. Prokaryotic organisms have one continuous molecule white eukaryotes have many (e.g. humans have 46). Viruses also contain nucleic acids and their genetic material can be either DNA or RNA. 

The tertiary structure of DNA depends on supercoihng. In prokaryotes, the circular DNA is twisted before the circle is sealed, giving rise to super-coiling. In eukaryotes, the supercoiled DNA is complexed with proteins known as histones. 

Thus far, we have been considering the secondary structure of DNA. double helices can fold up on themselves to form tertiary structures created by supercoiling. Supercoiling is most readily understood by considering covalently closed DNA molecules, but it also applies to DNA molecules constrained to be in loops by other means. Most DNA molecules inside cells are subject to supercoiling. 

The length of a DNA molecule is considerably greater than its diameter, and the extended molecule is quite flexible. A DNA molecule is said to be relaxed if it has no twists other than those imposed by its secondary structure. Put another way, relaxed DNA does not have a clearly defined tertiary structure. We consider two types of tertiary structure, one induced by perturbations in circular DNA, the other introduced by the coordination of DNA with nuclear proteins called histones. Tertiary structure in DNA, whatever the type, is referred to as supercoiling. 

Section 28.9 Within the cell nucleus, double-helical DNA adopts a supercoiled tertiary structure in which short sections are wound around proteins called histones. This reduces the effective length of the DNA and maintains it in an ordered anangement. 

Figure 4.19. Torsion constant a versus buffer concentration for supercoiled M13mp7 DNA in different buffers. All samples except that in 10 mM Tris contain 10 raW NaCl, so all have between 10 and 12 mM univalent positive ions. The sample in the middle contains only 10 mM NaCl. The numbers (1, 2, and 4) in the sample label refer to the gel electrophoretic mobilities, which reflect different tertiary structures, as described in the text. The a samples all contain varying amounts of Tris, while the b samples all contain citrate.

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. 

The quinolones and fluoroquinolones are thought to act on the bacterial enzyme deoxyribonucleic acid gyrase (DNA gyrase). This enzyme catalyses the supercoiling of chromosomal DNA into its tertiary structure. A consequence of this is that replication and transcription are inhibited and the bacterial cell s genetic code remains unread. At present, the mechanism by which these agents inhibit DNA gyrase is unclear. 

Levels of DNA Structure. A DNA molecule has several levels of structure ranging from the primary structure of the sequence of bases to the secondary structure of the Watson-Crick double helix to the tertiary structure resulting from folding or supercoiling the double helix to even higher order structures involved in the condensation of DNA in the cell nucleus. To serve as a basis for understanding the interaction of platinum complexes with DNA, we first describe some of the more important features of DNA structure. 

DNA supercoiling provides conformational potential energy for DNA tertiary structure formation such as the development of DNA cruciform structures (Figure 1.77). Supercoiling also leads to the creation of DNA triple helix (DNA triplex) structures, which form when an oligodeoxynucleotide chain, with an appropriately complementary deoxynucleotide residue... 

Figure 1.77 Schematic illustration of the influence of supercoiling on the formation of additional tertiary structure elements in closed circular DNA. (a) Double helical deoxynucleotide palindrome sequence (inverted repeat) that is a necessary prerequisite for cruciform formation (b) schematic diagram to show cruciform formation under conformational pressure of supercoiling as shown in (c) (d) more detailed ribbon cartoon to illustrate how phosphodiester backbones are "shared" at the cruciform junction (illustrations adapted from Sinden, 1994, Figs. 4.1, 4.3, 4.5 and 4.17 respectively).

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