Z-DNA, double helix

Drew H, Ihkano T, Duiaka S, Itakura K, Dickerson RE (1980) High-salt d(CpGpCpG) a left-handed Z DNA double helix. Nature (Lond) 286 567 - 573... 

FIGURE 12.13 (here and on the facing page) Comparison of the A-, B-, and Z-forms of the DNA double helix. The distance required to complete one helical torn is shorter in A-DNA than it is in B-DNA. The alternating pyrimidine-pnrine sequence of Z-DNA is the... 

The most striking conformational variant observed for a DNA double helix with Watson-Crick base pairing is referred to as the Z form. In Z DNA the backbone is twisted in the left-handed (counterclockwise) direction. This structure was first detected by Alex Rich and his co-workers (fig. 25.8). The Z form is a considerably slimmer helix than the B form and contains 12 bp/turn rather than 10. In the Z form, the planes of the base pairs are rotated approximately 180° with respect to the helix axis from their orientation in the B form (fig. 25.9). 

The effective charge Z of the disulfide derived from WR 1065, WR 33274, is near +4 and hence accumulates even more strongly near the DNA accounting for very effective OH scavenging. In addition, it protects DNA by compaction (Savoye et al. 1997). It is not homogeneously distributed along the DNA double helix. As a consequence, there are hot spots of protected and unprotected regions. 

G. Guzikevich-Guerstein and Z. Shakked. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nature Struct. Biol. 3 (1996) 32-7. 

Figure 2.27 (a) The DNA double helix. Dotted lines represent hydrogen bonded base-pair interactions (b) Idealised views of the three most common forms of DNA B, A and Z. Structures B and A have right-handed helicity with 10 and 11 phosphate residues per turn, respectively. The Z form is left-handed with 12 phosphates per turn. (Reproduced with permission from Academic Press). 

At the level of primary structure, several recent experiments have shown the effect of base sequence on the local structure of DNA. A dramatic example is the crystal structure of d(CpG) as determined by Rich and coworkers ( ). This molecule crystallizes in a left-handed double helical form called Z-DNA, which is radically different in its structural properties from the familiar right-handed B-DNA structure. Dickerson and Drew (10) showed in the crystal structure of the dodecanucleotide d(CGCGAATTCGCG) that the local twist angle of a DNA double helix varies with sequence. Deoxyribonuclease I cuts the phosphodiester backbone of the dodecanucleotide preferentially at sites of high twist angle (l 1). From these and other (12,13) experiments we see that the structure of DNA varies with base sequence, and that enzymes are sensitive to these details of structure. 

The dextrogyric rotation of the doublehelical DNA may generate the A-DNA, B-DNA, C-DNA, and D-DNA types, while the senestrogyric rotation generates the Z-DNA type. All these types are characterized by linear and angular steric parameters. Details on steric parameters, depending on the residual nucleotides from the macromo-lecular building and nucleobases pairs (respectively nucleotides) of the DNA double helix are provided below. 

Are there other possible conformations of the double helix Some variations on the usual representation of the double helix (B-DNA) are known to exist. In A-DNA, the base pairs lie at an angle to the helix axis, and in Z-DNA the helix is left handed, rather than the more usual right-handed form of B-DNA. These variant forms are known to have physiological roles. 

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. 

Z-DNA (Fig. 2b) presents the most striking example of how different from the B form the DNA double helix can be (Wang et. al., 1979 [87]). Although in Z-DNA the complementary strands are antiparallel like in B-DNA, unlike in B-DNA, they form left-handed, rather than right-handed, helices. There are many other dramatic differences between Z- and B-DNA (reviewed by Dickerson, 1992 [15]). 

The structure proposed by Watson and Crick was modeled to fit crystallographic data obtained on a sample of the most common form of DNA called B DNA Other forms include A DNA which is similar to but more compact than B DNA and Z DNA which IS a left handed double helix... 

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. 

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... 

The two strands, in which opposing bases are held together by hydrogen bonds, wind around a central axis in the form of a double helix. Double-stranded DNA exists in at least six forms (A-E and Z). The B form is usually found under physiologic conditions (low salt, high degree of hydration). A single turn of B-DNA about the axis of the molecule contains ten base pairs. The distance spanned by one turn of B-DNA is 3.4 nm. The width (helical diameter) of the double helix in B-DNA is 2 nm. 

The structures shown in Fig. 4-1 are for B-form DNA, the usual form of the molecule in solution. Different double-helical DNA structures can be formed by rotating various bonds that connect the structure. These are termed different conformations. The A and B conformations are both right-handed helices that differ in pitch (how much the helix rises per turn) and other molecular properties. Z-DNA is a left-handed helical form of DNA in which the phosphate backbones of the two antiparallel DNA strands are still arranged in a helix but with a more irregular appearance. The conformation of DNA (A, B, or Z) depends on the temperature and salt concentration as well as the base composition of the DNA. Z-DNA appears to be favored in certain regions of DNA in which the sequence is rich in G and C base pairs. 

Most DNA occurs in nature as a right-handed double-helical molecule known as Watson-Crick DNA or B-DNA (Fig I-1-9). The hydrophilic sugar-phosphate backbone of each strand is on the outside of the double helix. The hydrogen-bonded base pairs are stacked in the center of the molecule. There are about 10 base pairs per complete turn of the helix. A rare left-handed double-helical form of DNA that occurs in G-C-rich sequences is known as Z-DNA. The biologic function of Z-DNA is unknown, but may be related to gene regulation. 

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