Supercoil axis

The native form of chromatin in cells assumes a higher order stmcture called the 30-nm filament, which adopts a solenoidal stmcture where the 10-nm filament is arranged in a left-handed cod (Fig. 5). The negative supercoiling of the DNA is manifested by writhing the hehcal axis around the nucleosomes. Chromatin stmcture is an example of toroidal winding whereas eukaryotic chromosomes are linear, the chromatin stmctures, attached to a nuclear matrix, define separate closed-circular topological domains. 

Figure 14.1 Each polypeptide chain in the collagen molecule folds into an extended polyproline type II helix with a rise per turn along the helix of 9.6 A comprising 3.3 residues. In the collagen molecule three such chains are supercoiled about a common axis to form a 3000-A-long rod-like molecule. The amino acid sequence contains repeats of -Gly-X-Y- where X is often proline and Y is often hydroxyproline. (a) Ball and stick model of two turns of one polypeptide chain.

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 24-17 Negative and positive supercoils. For the relaxed DNA molecule of Figure 24-16a, underwinding or overwinding by two helical turns (Lk = 198 or 202) will produce negative or positive supercoiling, respectively. Note that the DNA axis twists in opposite directions in the two cases. 

The purple lines show the axis of the supercoil note the branching of the supercoil, (c) An idealized representation (c) of this structure. 

Fig. 3. Schematic representation of a tetrameric coiled coil, showing the main parameters. 0n marks the center of one a-helix, An the Ca position of a constituent residue, and Cn the superhelix axis n is the u-helix radius, r0 the superhelix radius, a the pitch angle, Q the pairwise helix-crossing angle, ip the positional orientation angle of a residue or phase of the helix, and to is the phase of the supercoil.

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. 

A new property appears in the conversion of a linear DNA molecule into a closed circular molecule. The axis of the double helix can itself be twisted into a superhelix (Figure 5.18B). A circular DNA molecule without any superhelical turns is known as a relaxed molecule. Supercoiling is biologically important for two reasons. First, a supercoiled DNA molecule has a more compact shape than does its relaxed counterpart. Second, supercoiling may hinder or favor the capacity of the double helix to unwind and thereby affects the interactions between DNA and other molecules. These topological features of DNA will be considered further in Section 27.3. 

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. ... 

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. 

An 84 bp segment of a circular DNA in the relaxed state would contain eight double-helical turns, or one for every 10.5 bp. If one of these turns were removed, there would be (84 bp)/7 = 12.0 bp per turn, rather than the 10.5 found in B-DNA (Fig. 24-14b). This is a deviation from the most stable DNA form, and the molecule is thermodynamically strained as a result. Generally, much of this strain would be accommodated by coiling the axis of the DNA on itself to form a supercoil (Fig. 24-14c some of the strain in this 84 bp segment would simply become dispersed in the untwisted struc-... 

---