Supercoiled double helix structure

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... 

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 24-12 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. 

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. 

There is a large variability possible in the structures of double stranded DNA due to the fact that (compared to polypeptides) many more bonds can be rotated in the backbone of each monomer (Scheme 14). The most common and physiologically most important structure is the B-DNA helix. It consists of two polynucleotide chains running in opposite direction which coil around a common axis to form a right-handed double helix. In the helix, the phosphate and deoxyribose units of each strand are on the outside, and the purine and pyrimidine bases on the inside. The purine and pyrimidine bases are paired by selective hydrogen bonds adenine is paired with thymine, and guanine with cytosine (Scheme 15). The structure is very flexible and can form a supercoil with itself, or around proteins. It can form a left-handed supercoil around histones to form nucleosomes which assemble in yet another helical structure to form chromatin. ... 

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. 

From procaryotes, such as coli, much simpler supercoiled DNA molecules c ui be isolated. These molecules, called plasmids (O, consist of a few thousand DNA base pairs joined in a closed circle. The double helix of such a circular molecule is supercoiled upon itself, to form a condensed structure, called "form... 

DNA is coiled in the form of a double helix, with both strands of the DNA coiling around an axis. The further coiling of that axis upon itself (Fig. 24-11) produces DNA supercoiling. As detailed below, DNA supercoiling is generally a manifestation of structural strain. When there is no net bending of the DNA axis upon itself, the DNA is said to be in a relaxed state. 

DNA consists of a double helix, with the two strands of DNA wrapping around each other to form a helical structure. To compact, the DNA molecule coils about itself to form a structure called a supercoil. A telephone cord, which connects the handpiece to the phone, displays supercoiling when the coiled cord wraps about itself. When the strands of a DNA molecule separate and unwind over a small local region (which occurs during DNA replication), supercoils are introduced into the remaining portion of the molecule, thereby increasing stress on this portion. Enzymes known as topoisomerases relieve this stress so that unwinding of the DNA strands can occur. 

The DNA molecule has a length considerably greater than its diameter it is not completely stiff and can fold back on itself in a manner similar to that of proteins as they fold into their tertiary structures. The double helix we have discussed so far is relaxed, which means that it has no twists in it, other than the helical twists themselves. Further twisting and coiling, or supercoiling, of the double helix is possible. 

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. 

Abstract The physical aspects of DNA structure and function are overviewed. Major DNA structures are described, which include the canonical Watson-Crick double helix (B form), B , A, Z duplex forms, parallel-stranded DNA, triplexes and quadruplexes. Theoretical models, which are used to treat DNA, are considered with special emphasis on the elastic-rod model. DNA topology, supercoiling and their biological significance are extensively discussed. Recent developments in the understanding of molecular interactions responsible for the stability of the DNA double helix are presented. 

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