Double helix supercoiling

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... 

Recent advances of the Seeman group led to the construction of a nanomechanical device from DNA [89]. In this molecular apparatus, the ion-dependent transition of B-DNA into the Z-conformation is used to alter the distance between two DNA DX domains attached to the switchable double helix. Atomic displacements of about 2-6 nm were attained. Ionic switching of nanoparticles by means of DNA supercoiling has also been reported [53]. Additional advances regarding the use of DNA is nanomechanical devices have been reported by Fritz et al., who showed that an array of cantilevers can be used to... 

A DNA molecule is said to be supercoiled when the ends of a DNA double helix join to form a closed circle which then winds back upon itself. 

In most DNA molecules the two ends of the DNA double helix are joined to form a closed circle. When this occurs the DNA then forms a supercoil by winding back on itself. Supercoiled DNA depends on the integrity of the closed circle. Any breaks in the circle will cause unwinding of the supercoil. 

Mitochondrial DNA and the DNA of most prokaryotes are closed circular structures. These molecules may exist as relaxed circles or as supercoiled structures in which the heUx is twisted around itself in three-dimensional space. Supercoiling results from strain on the molecule caused by under- or overwinding the double helix ... 

The Watson and Crick model for DNA as a double helix is only a generalized model to describe much more complex structures. Along with the typical double helix there exist structural elements such as supercoils, kinks, cruciforms, bends, loops, and triple strands as well as major and minor grooves. Each of these structural elements can vary in length, shape, location, and frequency. Even the simple DNA double helix can vary in pitch (number of bases per helical turn), sugar pucker conformation, and helical sense (whether the helix is left-or right-handed). 

Electron microscopy shows that DNA consists of either linear or circular structures. The chromosomal DNA in bacteria is a closed circle, a result of covalent joining of the two ends of the double helix (Figure 10.11). Note the presence of supercoils, branch points, intersections, and the generally thin and open structure. The chromosomal DNA in eukaryotic cells, like ours, is believed to be linear. 

FIGURE 24-11 Supercoiling of DNA. When the axis of the DNA double helix is coiled on itself, it forms a new helix (superhelix). The DNA superhelix is usually called a supercoil. 

FIGURE 24-12 Supercoiling induced by separating the strands of a helical structure. Twist two linear strands of rubber band into a right-handed double helix as shown. Fix one end by having a friend hold onto it, then pull apart the two strands at the other end. The resulting strain will produce supercoiling. 

Solving the problem of supercoils As the two strands of the double helix are separated, a problem is encountered, namely, the appearance of positive supercoils (also called supertwists) in... 

As the two strands of the double helix are separated, positive supercoils are produced in the region of DNA ahead of the replication fork. These interfere with further unwinding of the double helix. DNA topoisomerases Types I and II remove supercoils. Human topoiso-merase II is targeted by anticancer agents, such as etoposide, and DNA gyrase (a Type II topoisomerase found in E. coli that can introduce negative supercoils) is targeted by the antimicrobial quinolones. 

DNA supercoiling. The coiling of double helix DNA upon itself. 

RNA molecules consist of a single strand of nucleotides whilst DNA molecules consist of two nucleotide strands in the form of a supercoiled double helix. 

One of the most exciting biological discoveries is the recognition of DNA as a double helix (Watson and Crick, 1953) of two antiparallel polynucleotide chains with the base pairings between A and T, and between G and C (Watson and Crick s DNA structure). Thus, the nucleotide sequence in one chain is complementary to, but not identical to, that in the other chain. The diameter of the double helix measured between phosphorus atoms is 2.0 nm. The pitch is 3.4 nm. There are 10 base pairs per turn. Thus the rise per base pair is 0.34 nm, and bases are stacked in the center of the helix. This form (B form), whose base pairs lie almost normal to the helix axis, is stable under high humidity and is thought to approximate the conformation of most DNA in cells. However, the base pairs in another form (A form) of DNA, which likely occurs in complex with histone, are inclined to the helix axis by about 20° with 11 base pairs per turn. While DNA molecules may exist as straight rods, the two ends bacterial DNA are often covalently joined to form circular DNA molecules, which are frequently supercoiled. 

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