Z form of DNA

Also, local changes in the structural and chemical variation of DNA may have important effects on the overall extent of chromatin folding. For instance, transitions from the B to the Z form of DNA will result in nucleosome dissolution (as discussed earlier) and this could affect the folding of the fiber. As well, chemical modifications of the bases such as methylation have been shown to increase the folding of the chromatin fiber when linker histones are present [250] although the mechanism involved in this later case remains to be elucidated. 

In recent years an astonishing structural variety has been rmcovered for DNA. Crystal structures have shown that, apart from the structural motifs of the A-, B- and Z-forms of DNA, other, sequence-dependent structural variations exist which are observed when smaller sequence fragments are examined in detail. 

RGURE 8-19 Comparison of A, B, and Z forms of DNA. Each structure shown here has 36 base pairs. The bases are shown in gray, the phosphate atoms in yellow, and the riboses and phosphate oxygens inblue. Blueisthecolorusedto represent DNA strands i n I ater chapters. The table summarizes some properties of the three forms of DN A. 

Since the Z form of DNA is favored in regions rich in G-C pairs,118119 it is reasonable to expect that it may... 

A dramatically different form of the double helix has been observed in DNA containing alternating purine-pyrimidine sequences, especially d(CG)n but also d(TG)n. It is a left-handed, rather than a right-handed helix and is known as the Z form of DNA. Helix parameters are contrasted in Table 7.2 and space-filling models of the Z form and B form of DNA are compared below (Fig. 7-4.). 

In the Z form, the repeating unit is a dinucleotide and the resultant structure has the staggered zig-zag shape of the sugar-phosphate backbone from which the name (Z) was derived. It is possible that the Z form of DNA does have an important biological role although at present this is uncertain. Though sequences of d(TG) where n >25 are common in eukaryotic DNA ( 105 copies in the human genome), it has not been shown if they adopt the Z form in vivo. 

List three of the major structural differences between the B and Z forms of DNA. 

On another way, single-stranded DNA is a poor substrate 15,31) and the Cu(phen)2/H202 system cleaves A, B, and Z forms of DNA at different rates 32). The B structure is the most easily cleaved DNA. A DNA is less efficiently cleaved presumably because of fewer favorable contacts between the complex and the widened minor groove of the A form double helix. The A structure, formed by RNA-DNA hybrids, is cleaved on both strands at roughly one-third of the rate for B DNA under comparable conditions. In contrast, the left-handed Z structure, with its deep narrow minor groove, is completely resistant to Cu(phen)2 degradation. 

Two other forms of DNA are the A-form and the Z-form (see Figure 28.2). If the relative humidity of the P-form of DNA decreases to 75% and the sodium chloride concentration drops to below 10%, the P-form is transformed into the A-form helix. The A-form is a right-handed helix with 11 base pairs per complete turn and a helical pitch of about 28° however, a 20° tilt to the base-pair planes leads to a displacement from the central axis (see Figure 28.2). The Z-form of DNA adopts a left-handed helix, but it is not simply the mirror image of the P /orm or the A form helices. The Z-form has 12 base pairs per complete turn and a helical pitch of about 45 A it has a wide, shallow major groove and a narrow, deep minor groove. ... 

Figure 28.2 A-, B-, and Z-forms of DNA. (Hecht, S. M., ed. 1996. Bioorganic chemistry Nucleic acids, 10-11, Figure 1-9. New York Oxford University Press. By permission of Oxford...

The comparison of geometrical parameters of nucleotides in equilibrium and DNA-like corrformations (Tables 5.9-5.11) indicates that the changes of corrfor-mations of the considered species do not lead to their appreciable variations. The only significant difference revealed is related to the C-O bond lengths within the C4 -04 -Cr fragment. In the case of Z-forms of DNA considerable increase of these bond lengths (A =0.028-0.057 A) is predicted. This is usually explained by strengtherung of anomeric interactions. 

Yet another has been devised, based on a switch from a right- to a left-handed helix (B- to Z-form of DNA), which can be brought about merely by the addition of different ions (magnesium, for example). Considering the variety of proteins that interact with DNA—which break the chain or seal the breaks, replicate the... 

MD studies on B and Z forms of DNA with explicit waters and explicit counterions were reported by Swamy and Clementi.i G-C and A-T decamer sequences in their B forms were surrounded by a rectangular box with 1500 water molecules and 20 K+ ions. In addition, a G-C dodecamer in its Z form with 1851 water molecules and 24 K+ ions was studied. Water molecules in these studies were four-centered MCY waters. These simulations were carried out for a total of 7 ps, with the first 3 ps serving as an equilibration period. The DNA in all cases was rigid, and only the ions and the waters were allowed to execute motions. The dynamical behavior of those ions showed them to be strongly bound to the DNA with restricted mobilities, a conclusion different from what counterion condensation theory and other simulations tend to suggest. The exploration of space by the counterions around DNA in the short time scale of this study was insufficient to permit the derivation of general conclusions about the ion mobilities, however. 

Figure 10.1 (a) Secondary structures of, from left to right, A-, B-and Z-forms of DNA. Ball and stick representation with the phosphate backbones highlighted (taken from www. biochemistry.ucla.edu/biochem/Faculty/ Martinson/Chime/abz dna/abz master.html, last accessed 28/07/2008) and (b) transition from double-stranded DNA (ds-DNA) to single-stranded random coil DNA (ss-DNA). 

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