Section 23.3.2.1. Backbone geometry

Before making detailed comparisons of the three helix types, one must define the parameters by which the helices are characterized. The fundamental feature of all varieties of nucleic acid double helices is two antiparallel sugar–phosphate backbone chains, bridged by paired bases like rungs in a ladder (Fig. 23.3.2.1). Using the convention that the positive direction of a backbone chain is from 5′ to 3′ within a nucleotide, the right-hand chain in Fig. 23.3.2.1 runs downward, while the left-hand chain runs upward. A- or B-DNA is then obtained by twisting the ladder into a right-handed helix. But Z-DNA cannot be obtained from Fig. 23.3.2.1 simply by giving it a left-handed twist; both backbone chains run in the wrong direction for Z-DNA. A more complex adjustment is required, and this will be addressed again later.

Figure 23.3.2.1| top | pdf | Unrolled schematic of A- or B-DNA, viewed into the minor groove. Paired bases are attached to backbone chains that run in opposite directions: downward on the right and upward on the left. Z-DNA differs from A- and B-DNA in that the two backbone chains run in opposite directions from those shown here. Hence, Z-DNA cannot be obtained from A- or B-DNA by simple twisting around the helix axis.

The conformation of the backbone chain along each nucleotide is described by six torsion angles, labelled α through ζ, as shown in Fig. 23.3.2.2. An earlier convention termed these same six angles as ω, φ, ψ, ψ′, φ′, ω′ (Sundaralingam, 1975), but the alphabetical nomenclature is now generally employed. Torsion angles are defined in Fig. 23.3.2.3, which also shows three common configurations: gauche ⁻ (−60°), trans (180°) and gauche ⁺ (+60°). These three configurations are especially favoured with sp³ hybridization or tetrahedral ligand geometry at the two ends of the bond in question, because their `staggered' arrangement minimizes ligand–ligand interactions across the bond. An `eclipsed' arrangement with ligands at −120°, 0° (cis), and 120° is unfavourable because it brings substituents at the two ends of the bond into opposition. Table 23.3.2.1 lists the mean values and standard deviations of all six main-chain torsion angles for A-, B- and Z-DNA, as recently observed in 96 oligonucleotide crystal structures (Schneider et al., 1997).

Table 23.3.2.1| top | pdf | Average torsion-angle properties of A-, B- and Z-DNA (°) Values listed are mean torsion angles, with standard deviations in parentheses. Conformations are only approximate; — indicates a non-gauche/trans conformation. BII and ZII are less common variants. For δ, the sugar ring geometry is quoted in place of gauche/trans. χ for B-DNA combines pyrimidines and purines. Values were obtained from a sample of 30 A-DNAs, 34 B-DNAs, 22 Z-DNAs and ten nonstandard DNAs in the Nucleic Acid Database. From Schneider et al. (1997).   A-DNA 293 (17) 174 (14) 56 (14) 81 (7) 203 (12) 289 (12) 199 (8) Conformation g− t g+ C3′-endo t g− t B-DNA 298 (15) 176 (9) 48 (11) 128 (13) 184 (11) 265 (10) 249 (16) Conformation g− t g+ C1′-exo t g− g−                 BII-DNA   146 (8)   144 (7) 246 (15) 174 (14) 271 (8) Conformation   —   C2′-endo g− t g− ZI-DNA – purines 71 (13) 183 (9) 179 (9) 95 (8) 95 (8) 301 (16) 63 (5) Conformation g+ t t O4′-endo g+ g− g+                 ZII-DNA – purines         189 (12) 52 (14) 58 (5) Conformation         t g+ g+                 ZI-DNA – pyrimidines 201 (20) 225 (16) 54 (13) 141 (8) 267 (9) 75 (9) 204 (98) Conformation t — g+ C2′-endo g− g+ t                 ZII-DNA – pyrimidines 168 (16) 166 (14)           Conformation t t

Figure 23.3.2.2| top | pdf | Sugar–phosphate backbone of RNA and DNA polynucleotides. One nucleotide begins at a phosphorus atom and extends just short of the phosphorus atom of the following nucleotide, with the conventional positive direction being PO5′—C5′—C4′—C3′—O3′P, as indicated by the arrows. Main-chain torsion angles are designated α through ζ, and torsion angles about the five bonds of the ribose or deoxyribose ring are through , as shown. If one imagines atoms O3′—P—O5′ as a hump-backed bridge, as one crosses the bridge in a positive chain direction, oxygen atom O1 is to the left and O2 is to the right. These oxygens, accordingly, are sometimes designated OL and OR. The —OH group attached to the C2′ atom of the ribose ring in RNA shown here is replaced by —H in the deoxyribose ring of DNA. Atom N to the right is part of the base attached to the sugar ring: N1 in pyrimidines and N9 in purines. Torsion angle χ is defined by O4′—C1′—N1—C2 in pyrimidines and O4′—C1′—N9—C4 in purines.

Figure 23.3.2.3| top | pdf | Definition of torsion angles. A positive angle results from clockwise rotation of the farther bond, holding the nearer bond fixed. Torsion angle +60° is designated as gauche+ or g+, angle 180° is trans or t and angle −60° is gauche− or g−.