Helical axis

Figure 7.2 Three helical forms of DNA, each containing 22 nucleotide pairs, shown in both side and top views. The sugar-phosphate backbone is dark the paired nucleotide bases are light, (a) B-DNA, which is the most common form in cells, (b) A-DNA, which is obtained under dehydrated nonphysiological conditions. Notice the hole along the helical axis in this form, (c) Z-DNA, which can be formed by certain DNA sequences under special circumstances. (Courtesy of Richard Feldmann.)...

In B-DNA because the helical axis runs through the center of each base pair and the base pairs are stacked nearly perpendicular to the helical axis (see Figures 7.1 and 7.5), the major and minor grooves are of similar depths. 

Figure 6. Projection of the 7/3 helical conformation of PDPS onto a plane normal to the helical axis. Silicon atoms are represented by the larger filled circles, carbon atoms by the smaller.

Fig. 1 The w-stack of double helical DNA. In this idealized model of B-DNA the stack of heterocyclic aromatic base pairs is distinctly visible within the sugar-phosphate backbone (schematized by ribbons) a view perpendicular to the helical axis b view down the helical axis. It is the stacking of aromatic DNA bases, approximately 3.4 A apart, that imparts the DNA with its unique ability to mediate charge transport. Base stacking interactions, and DNA charge transport, are exquisitely sensitive to the sequence-depen-dent structure and flexibility of DNA...

Krimm, 1968a,b Mattice and Mandelkern, 1971 Krimm and Tiffany, 1974). This conformation is similar to that of a single strand from collagen, with average backbone dihedrals of (0,0) = ( 75°, +145°). These dihedrals lead to an extended left-handed helical conformation with precisely three residues per turn and 9 A between residues i and i + 3 (measured Cft to C/3). A cartoon of a seven-residue alanine peptide in this conformation is shown in Figure 1. Notably, backbone carbonyl and amide groups point perpendicularly out from the helical axis into the solvent and are well-exposed. 

The stereoselected Cda conformation of the BPDE i(-) and Il(-) adducts to N6(a) were chosen for study in a reoriented complex with an externally bound pyrene moiety. In Figure 13, the adduct is shown in its optimum orientation in B-DNA with adenine after an anti - syn transformation for which the non-bonded contacts are poor, and with the normal anti base orientation with favorable contacts. The fit improves for the anti base as ax 30°. The orientation of the pyrene moiety is a(BPDE) =31° and the local helical axis of the DNA is oriented at y(DNA) = 15° Calculations were not performed with externally bound BPDE-DNA adducts to 06(G) and NU(C). Calculations of externally bound BPDE I(-)-N6(a) adducts with kinked DNA with ax + 30° yields an orientation a(BPDE) = 31° in good agreement with experimental results for the externally bound component (51). 

The distance between two subsequent base pairs along the helical axis is called helical rise (/ ). The pitch (P) is the length of the helix axis for one complete helix turn. The turn angle per nucleotide or twist angle (t) is given by 360°/number of nucleotides per turn. Data describing some properties of A, B, and Z DNA structure are found in Table 2.3 as adapted from Table 1.10 of reference 13 and the Jena image library website address above. 

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