Section 23.3.3.1.  x displacement and groove depth

A-DNA (Wahl & Sundaralingam, 1996, 1998), B-DNA (Berman, 1996; Dickerson, 1998b) and Z-DNA (Ho & Mooers, 1996; Basham et al., 1998) have each been the subject of recent reviews, to which the reader is referred for details that cannot be covered here. The distinctive properties of the three helices are listed in Table 23.3.3.1. The most obvious distinction is handedness: A and B are right-handed helices, whereas Z is left-handed. Moreover, the position of each base pair relative to the helix axis is quite different. As noted in Fig. 23.3.2.13, the helix axis passes through base pairs in B-DNA, lies on the minor groove side of base pairs in Z-DNA, and on the major groove side in A-DNA. In terms of the helix parameters of Fig. 23.3.2.12, A-DNA has a typical x displacement of d_x = +3 to +5 Å, B-DNA has d_x = −1 to 0 Å, and Z-DNA has d_x = −3 to −4 Å. There is virtually no overlap between these three ranges; x displacement, d_x, in fact, is a better criterion for differentiating the three classes of helix than is sugar ring conformation.

Table 23.3.3.1| top | pdf | Comparison of structures of A, B and Z helices   A B Z Handedness Right Right Left Helix axis relative to base pairs Major groove side Through centre of base pair Minor groove side Major groove Very deep and narrow Wide, same depth as minor Very shallow and broad Minor groove Shallow and broad Variable, same depth as major Very deep and narrow Glycosydic bonds anti anti C: anti       G: syn Minor groove backbone chain sense † Clockwise Clockwise Counterclockwise Sugar conformation C3′-endo (narrow range) C1′-exo/C2′-endo (broad range) C: C2′-endo       G: C3′-endo Base pairs per helix repeat 1 1 2 Base sequence limitations None None Alternating or close variants Rise per base pair (average) 2.9 Å 3.4 Å C-G: 4.1 Å       G-C: 3.5 Å Base pair inclination 10–20° ca 0° ca 0° Mean twist angle 30–33° 34–36° C-G: −8°       G-C: −52° Helix repeats per turn 11–12 10–10.5 6 (2 base pairs) Propeller twist Often substantial, 0–25° Often substantial, 0–25° Usually small Common biological occurrence RNA DNA None? †Relative 5′-to-3′ directions of the two backbone chains, when viewed into the minor groove.

A direct consequence of these x displacement values is great differences in depths of major and minor grooves. Both grooves are of equivalent depth in B-DNA because base pairs sit on the helix axis. In A-DNA, a base pair is pushed off-axis so that its minor edge approaches the helix surface, making the minor groove very shallow and the major groove cavernously deep. In Z-DNA, it is the major edge of each base pair that is pushed toward the surface, so that the minor groove is deep and the major groove is so shallow as hardly to be characterized as a groove at all. It is sometimes stated that `Z-DNA has no major groove', but space-filling stereos, such as Fig. 1 of reference Z6 or Fig. 3 of Z23 reveal the shallowest of major grooves running around the helix cylinder, flanked by very slightly higher phosphate backbones.