Double helix pitch

Free" myosin molecules associate spontaneously into bundles like Aose in the muscle cell. The molecule is one of the longest Imown in nature (155 nm) with twin-heads extending from the bimdle in a helical fashion and the tail consisting of a coiled coil double helix (pitch 7.5 nm). The distal part of this tail (110 nm) forms the bimdle and the heads are pointed outwards by a "hinge" (45 nm). The period between the heads along the axis of a bundle is 14.3 run. 

For helical ribbon stirrers not only the power characteristic but also the mixing time characteristic is clearly dependent upon the size of the helical surface (single or double helix pitch 0.5 or 1.0). For the range Re < 100 it was found that ... 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

Extrapolation of the molecular structure of an a-maltohexaose duplex com-plexed with triiodide in single crystals leads to a left-handed, 8-fold, antiparallel double-helix for amylose.90 The pitch of this idealized helix is 18.6 A, so h is only 2.33 A. Although this model is no contender to the fiber data, in terms of biosynthesis, it is doubtful that the native amylose helix favors antiparallel chains. 

Intercalating agents are hydrophobic, planar structures that can fit between the DNA base pairs in the center of the DNA double helix. These compounds (ethidium bromide and actinomycin D are often-used examples) take up space in the helix and cause the helix to unwind a little bit by increasing the pitch. The pitch is a measure of the distance between successive base pairs. 

The unit cell is orthorhombic, with a = 11.4 A (1.14 nm), b = 9.8 A (980 pm), and c — 33.7 A (3.37 nm). A double helix was proposed in which two identical, left-handed strands are antiparallel to one another. Each strand has four disaccharide residues per pitch length. 

The fiber axis repeat distance is 24.6 A (2.46 nm). The molecule is a double helix. The individual chains contain 3 disaccharide residues in one complete turn of pitch 24.6 A (2.46 nm). 

Agarose and its O-methyl, sulfate, 0-(2-hydroxyethyl), and 0-(car-boxyethylidene) derivatives give diffraction diagrams corresponding to a common molecular structure. A double helix having an axial periodicity of 9.5 A (950 pm) was proposed. Each chain in the double helix is a left-handed, threefold helix of pitch 19.0 A (1.90 nm), and it is translated axially, relative to its partner, by 9.5 A (950 pm). 

There are two distinct stereochemical possibilities for the helix which are consistent with the intensity distribution. One of them is a 2-fold single-helix of pitch 19.6A and the other a 4-fold, half-staggered, parallel, double-helix of pitch 39.2A. The doublehelix could be right- or left-handed. In all cases, there is considerable conformational mobility about the (1- 6) linkage of the disaccharide side chain. Preliminary models have been built for each possibility and, due to insufficient diffraction data, detailed x-ray refinements have not been conducted for any of them. 

Using the pitch, symmetry, monomer geometries and other stereochemical constraints, a number of types of molecular model can be constructed. Typical dilemmas are whether the molecular helix is left- or right-handed, whether the molecule is a single helix or coaxial double-helix (and in the later case whether the two chains in the duplex are parallel or antiparallel), or whether, if there are two or more molecules in the unit cell, the molecules are parallel or antiparallel. Solution of a structure therefore involves refinement and adjudication All candidate models are refined until the fit with the measured x-ray amplitudes or steric factors allows one model to be declared significantly superior to the others by some standard statistical test. 

In the Z-conformation (3), which can occur within GC-rich regions of B-DNA, the organization of the nucleotides is completely different. In this case, the helix is left-handed, and the backbone adopts a characteristic zig-zag conformation (hence Z-DNA ). The Z double helix has a smaller pitch than B-DNA. DNA segments in the Z conformation probably have physiological significance, but details are not yet known. 

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). 

The diameter of the double helix of B-DNA, measured between phosphorus atoms, is just 2.0 nm. The rise per turn, the pitch, is 3.4 nm. There are about ten base pairs per turn (9.7 and 10.6 in two different crystal forms).68 69 Thus, the rise per base pair is 0.34 nm, just the van der Waals thickness of an aromatic ring (Table 2-1). It is clear that the bases are stacked in the center of the helix. A 1000-bp (1-kb) gene would be a segment of DNA rod about 340 nm long, about 1/40 the length of the molecule in the electron micrograph of Fig. 5-13. 

The duplex is a right-handed double helix with 10 bases per turn. The diameter of the helix is 20 A (2 nm) and the pitch is 34 A (3.4 nm). The sugar-phosphate backbone is on the outside of the helix, and the two antiparallel chains are connected by the hydrogen-bonded bases. The DNA in prokaryotes and eukaryotes is generally found in the duplex form, although there are some single-stranded DNA viruses. DNA is a very robust molecule in comparison with many proteins. The simple double-helical secondary structure is readily reassembled after denaturation, unlike the complex tertiary protein structures that can denature... 

Mou, J., Czajkowsky, D.M., Zhang, Y. and Shao, Z. (1995) High-resolution atomic-force microscopy of DNA the pitch of the double helix. FEES Lett., 371, 279-282. 

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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