Z-DNA structures

FIGURE 12.14 Comparison of the deoxy-guanosine conformation in B- and Z-DNA. In B-DNA, the Cl -N-9 glycosyl bond is always in the anti position (lefi). In contrast, in the left-handed Z-DNA structure, this bond rotates (as shown) to adopt the syn conformation. 

Poly(dG-dC) poly(dG-dC) and its methylated analogue structures assume left-handed conformation (Z-DNA) in high molar sodium salt (Na", K" ), in low molar divalent cations (Ca", Mg", Ni ), micromolar concentrations of hexaamine cobalt chloride (Co(NH3)6)Cl3 and in millimolar concentrations of polyamines. In order to analyse the binding of berberine to Z-form DNA, Kumar et al. [186] reported that the Z-DNA structure of poly(dG-dC) poly(dG-dC) prepared in either a high salt concentration (4.0 M) or in 40 mM (Co(NH3)6)Cl3 remained invariant in the presence of berberine up to a nucleotide phosphate/alkaloid molar ratio of 0.8 and suggested that berberine neither bormd to Z-form DNA nor converted the Z-DNA to the... 

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. 

A, B, and Z DNA structure are found in Table 2.3 as adapted from Table 1.10 of reference 15 and the Jena image library at http //www.imb-jena.de/IMAGE DNA MODELS.html. 

In contrast to RNA, DNA is polymorphic. Under low salt conditions or at high relative humidity, DNA adopts the B-form usually considered to be biologically active. With increasing addition of salt or of polar organic solvents (synonymous with reduced relative humidity or removal of available water of hydration), and with certain types of counterions, DNA and double-stranded synthetic polynucleotides transform from B-DNA to the A-, C-, D-, Z-forms (see Thble 24.1 and Fig. 24.1. Only the A-, B- and Z-DNA structures, which have thus far been determined in detail by single crystal diffraction methods, are of structural interest and they are considered in the following sections. 

With these notes of caution, X-ray crystallographic studies have provided important insights into the patterns of hydration of the A-, B-, and Z-conformations of DNA. In a seminal work, based on 15 B-DNA, 22 A-DNA, and 22 Z-DNA structures, Schneider et al. (17) have determined the average number of water molecules located in the first hydration shells of phosphates and bases of A-, B-, and Z-form DNAs. It has been found that the sum of the waters in the hydration shells of phosphates and bases coincides with the net number of ordered waters in A- and B-DNA. This agreement is consistent with a picture in which the hydration shells of phosphate groups and bases in DNA do not overlap. By contrast, the sum of phosphate and base waters in Z-DNA (6.8) is larger than the total number of ordered waters (5.3), which suggests an overlap between the hydration shells of the backbone and the bases. The latter... 

The left-handed Z-DNA structure of poly[d(A-T)] poly[d(A-T)] as well as poly[d(A-C)] poly[d(G-T)] in the presence of Ni ions leads to characteristic IR and Raman spectra. Markers for these particular double-helical secondary structures are Raman frequency (phos-phodiester chain vibration at 746 and 815 cm syn geometry of the purines evidenced by a breathing mode coupled to the deoxyribose vibration at 622 cm a characteristic profile in the 1300-1400 cm region with a shift of the 1374 cm purine line lo lower wavenumbers correlated with the antijsyn reorientation of the nucleosides under the B - Z transition. " ... 

A. Herbert and A. Rich. 1999. Left-handed Z-DNA Structure and Function Genetica 106 37-47. (PubMed)... 

Chili, r. K., and Dickerson, R, K. 2000, 1 A crystal slrucLures of B-12NA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium, j. Mol. Biol.. 101 915-945. Herbert, A, and Rich, A. 1999. Left-handed Z DNA Structure and tunction. Genetica 105 37—47. 

Small Molecules that Induce and Stabilize Z-DNA Structures... 

---