DNA, Z-form

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 interstrand cross-link also induces DNA bending.72 X-ray and NMR studies on this adduct show that platinum is located in the minor groove and the cytosines of the d(GC) base pair involved in interstrand cross-link formation are flipped out of the helix stack and a localized Z-form DNA is observed.83-85 This is a highly unusual structure and very distorting—implications for differential repair of the two adducts have been addressed. Alternatively, the interstrand cross-link of the antitumor inactive trans-DDP is formed between a guanine (G) and its complementary cytosine (C) on the same base p a i r.86,87/ nms- D D P is sterically incapable of producing 1,2-intrastrand adducts and this feature has been cited as a dominant structural reason for its lack of antitumor efficacy. It is clear that the structural distortions induced on the DNA are very different and likely to induce distinctly different biological consequences. 

Z-form DNA is a more radical departure from the B structure the most obvious distinction is the left-handed helical rotation. There are 12 base pairs per helical turn, and the structure appears more slender and elongated. The DNA backbone takes on a zigzag appearance. Certain nucleotide sequences fold into left-handed Z helices much more readily than others. Prominent examples are sequences in which pyrimidines alternate with purines, especially alternating C and G or 5-methyl-C and G residues. To form the left-handed helix in Z-DNA, the purine residues flip to the syn conformation, alternating with pyrimidines in the anti conformation. The major groove is barely apparent in Z-DNA, and the minor groove is narrow and deep. 

With adequately tailored short Z-form DNA duplexes, H-transfer occurs by intrastrand P-H2 -abstraction [reaction (44) Kawai and Saito 1999 Kawai et al. 2000a], while competitive HI - and a-H2 -abstractions occurs in B-form DNA (Sugiyama et al. 1990,1993, 1996). Predominant Hl -abstraction is observed in a DNA-RNA hybrid (Sugiyama et al. 1997). 

In the case of sensitization of halouracil-containing DNA with ionizing radiation, attention has been drawn to potential contributions of resonant electron capture of low-energy electrons (Abdoul-Carine et al. 2001). The reaction of eaq with 8-Br-dGuo (Chap. 10.7) incorporated into DNA leads to a conversion of 8-Br-G into G in high yields with Z-form DNA being more effective than B-form DNA (Kimura et al. 2004). 

Abdou IM, Sartor V, Cao H, Schuster GB (2001) Long-distance radical cation migration in Z-form DNA. J Am Chem Soc 123 6696-6697... 

The first observation of VCD in small model DNA molecules, and in large deoxynucleic acid models, was reported by us in 1989 [18]. The VCD signals in the 1550 to 1750 cm"1 spectral region were found to be similar to those observed for the RNA reported earlier. In addition, our first report on DNA models also contained the observation of B and Z form DNA, along with the DECO equations and model calculations of the helical polymers. Subsequently, VCD was reported for poly(dG-dC) poly(dG-dC), poly(dG) poly(dC), poly(dA-dT) poly(dA-dT) and poly(dA) poly(dT) in the B-conformation in buffered, aqueous solution [22]. Differences were observed for DNA models, depending on the base composition and sequence, and the observed results were quantitatively interpreted in terms of the exciton model for coupled carbonyl stretching vibrational states. 

Figure 13. VCD (top) and infrared absorption spectra (bottom) of poly(dG-dC) poly(dG-dC) in high salt (NaCl) solution (Z-form DNA)...

Recent progress in confocal micro Raman spectroscopy has made it possible to investigate chromosomes and whole single living cells (Puppels et al., 1990, 1991). A spatial resolution of less than 1 )im was obtained. Different Raman spectra have been recorded of the cytoplasm and the cell nucleus. The spectrum of the nucleus consists of lines attributed to DNA and protein vibrations, strongly ressembling the spectra of isolated chromatin. The search for left-handed Z form DNA in metaphase chromosomes is in progress. 

The most striking structure that has been observed for a DNA duplex is the left-handed Z-form DNA having Watson-Crick base pairing and a zigzag sngar phosphate... 

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... 

Halo-dU derivatives have been used in DNA duplexes as they undergo photochemical crosslinking reactions. 5-Iodo-dU has been used in crosslinking reactions in Z-form DNA, and 4-thio-5-bromo-dU has also been prepared and incorporated into ODNs where it was demonstrated that cells containing it became sensitive to UVA light. The formation of a crosslink between Br-dC and dG has also been reported. 5-Iodo pyrimidines as well as 7-iodotuberci-din have been used for post-synthesis modification whilst on solid support for Pd-catalysed substitution by an alkynylated spin label. ... 

Charge transport was studied through photo-oxidation of the natural B-form duplex attached to a Ti02/Dopamine complex at the 5 terminal of the sense strand. This B-form was converted to Z-form DNA by adding a solution of high salt concentration — 20 mM Co(NH3)6Cl3 — which stabilizes the DNA in the Z-form, The experiments were... 

Substitution within a short DNA duplex amenable to Z-form DNA of two contiguous L-nucleotides stabilised the left-handed Z-conformation. The l-nucleotides induced, at low salt concentration, a local left-handed conformation different from the existing Z-DNA, but which contributed to the lower energy required for B- to Z-transition. The role of the 3 -5 exonuclease activity of the tumour suppressor p53 protein has been examined by an in vitro assay in which ODNs were terminated with either p-D or P-l of ddAMP or 3 -thio-ddc (SddC). °° The affinity of the p53 protein was shown to be five-fold lower for P-l nucleotides. 

Table 1.2 Summary of all the main differences between B-, A- and Z-form DNA in terms of dimensions, angles and conformations.

Other than B-form DNA, there are other forms of DNA that are more distorted from Watson and Crick ideality. These include A-form, C-form, D-form and T-form DNA. Of these, A-form DNA is the most similar to B-form DNA (Figure 1.73). The only major difference is that the 2 -deoxy-/3-D-ribofuranose rings of A-form DNA exist in an alternative C -endo twist conformation (Figures 1.71 and 1.73). Consequently, the helix diameter is wider and there are 11 base pair residues per turn (Table 1.2). A-form DNA also possesses shallow major and minor grooves. Z-form DNA, by contrast, is radically different from B-form... 

DNA (Table 1.2) (Figure 1.74). The helbc sense of Z-form DNA is now left handed and the backbones of the two poly deoxynucleotide chains map out a zigzag spiral path. This results from the tendency of deoxyguanosine nucleotide residues to distort so that their 2 -deoxy-/3-D-ribofuranose rings adopt a C -endo instead of C -endo twist conformation (Figure 1.71). However, in addition, the guanine bases move to a syn conformation (positioned over the top of their attached furanose rings), instead of the more usual anti conformation... 

Figure 1.74 Depiction of Z-form DNA. (pdb 331d) using Rings Display (side view) in which the anti-parallel phosphodiester backbones are shown as arrowed ribbons (green) ribose rings (green), purine bases (red) and pyrimidine (blue). This side view demonstrates how the phosphodiester backbone now takes on a "zig-zag" appearance, hence the name of this DNA conformation. This double helix is now left-handed.

Figure 1.75 Z-form DNA results from wholesale conformational changes in deoxyguanosine nucleotide (dpG) residues. The more usual anti, +sc, C2 endo nucleotide conformation gives way to a syn, ap, C3 endo conformation, (a) Illustration of syn dpG conformation, (b) Ball and stick depiction of pdG(syn, ap, C3 endoj.pdC base pair as found in Z-form DNA.

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