BDNA to ZDNA Transition and Stabilization

Molecular structure of left-handed Z-DNA was established 25 yr ago by single crystal X-ray crystallography of alternating purine/pyrimidine sequences (16). Z-DNA has a zig-zag arrangement of the sugar phosphate backbone with only deep minor grooves and no discernible major groove (Fig. 4). In contrast, the phosphate groups lie on a smooth helical line in B-DNA with minor and major grooves. Initially, Z-DNA was thought to be a nonphysiological structure, because 3 to 4 MNaCl was required to induce Z-DNA in solution. However, later studies revealed that |iM concentrations of polyamines could convert B-DNA to Z-DNA in alternating purine/pyrimidine

Fig. 4. The "information-rich" residues that allow sequence-specific recognition of the major groove of the B-DNA lie on the convex surface of left-handed Z-DNA helix. The two DNA strands of each duplex are highlighted by a solid black line. The "zigzag" nature of the Z-DNA backbone is clearly seen (Reprinted from ref. 16; permission conveyed through Copyright Clearance Center, Inc.).

Z-DNA B-DNA

Fig. 4. The "information-rich" residues that allow sequence-specific recognition of the major groove of the B-DNA lie on the convex surface of left-handed Z-DNA helix. The two DNA strands of each duplex are highlighted by a solid black line. The "zigzag" nature of the Z-DNA backbone is clearly seen (Reprinted from ref. 16; permission conveyed through Copyright Clearance Center, Inc.).

sequences (30). The fluctuating concentrations of polyamines and supercoiling of transcriptional domains might work together with DNA sequence-specificity in inducing and propagating Z-DNA. Indeed, the intrinsic affinity of spermine for Z-DNA was found to be 10-fold higher for d(CA/TG) than for d(CG) dinucleotide, and both greater than that of B-DNA (31).

The packing of spermine-DNA complexes in a pure-spermine form of Z-DNA crystals suggested that the molecular basis for the tendency of spermine to stabilize compact DNA structures derived from the capacity of spermine to interact simultaneously with several duplexes. This capacity is maximized by the flexibility of the methylene-bridging regions of spermine. The length and flexibility of spermine and the dispersion of charge-charge, hydrogen-bonding, and hydrophobic-bonding potential throughout the molecule maximize the ability of spermine to interact simultaneously with different DNA molecules. Although major and minor groove binding of spermine to DNA have been demonstrated in various studies, recent modeling studies emphasize the mobility

Fig. 5. Views into the major groove of d(G-C)5/d(G-C)5 with spermine in place before (A) and after (B) energy minimization. Note the decrease in distance across the major groove (■) and the increase across the minor groove (•) after energy minimizations was performed. Squares and circles represent the same points on the helix, and are included for comparison between (A) and (B). (Reprinted with permission from ref. 33.)

of the spermine molecule between major and minor grooves and phosphate backbone binding sites (32). The competition of polyamines with monovalent and divalent cations, the width and other spatial parameters of major and minor grooves, and the functional groups of base sequence are all involved in "fixing" the polyamine binding sites. For example, the conformational energy calculations of Feuerstein et al. (33) indicate maximal interactions between proton acceptors on the oligomer and proton donors on spermine (Fig. 5). When spermine was docked into the major groove of

B-DNA, dynamic changes in DNA structural parameters, such as DNA bending over the major groove containing spermine, alterations in oligomer sugar puckering, and interstrand phosphate distances, occurred. Although the sequence used has the capacity to form Z-DNA, the experimental parameters were set for B-DNA. In contrast, structures of Z-DNA in which the crystals are produced in the presence of spermine, shows that the high prevalence of minor grooves and the rigidity of the Z-DNA backbone structure provides opportunity for minor groove binding of the spermine in d(CGCGCG)2 hexamer crystals (34). Thus, crystal structure analysis and molecular modeling studies provide data for the specific contexts revealing the preferential binding of spermine to major or minor grooves of DNA.

Behe and Felsenfeld (30) first showed that physiologically compatible concentrations of spermidine and spermine could induce and stabilize the Z-DNA. Thomas and Messner 35) further investigated the structural specificity effects of spermidine homologs in the induction and stabilization of the Z-DNA for poly(dG-m5dC)/poly(dG-m5dC). They found that spermidine was fourfold more efficient than a homolog with two additional -CH2-groups in the methylene chain, in inducing and stabilizing the Z-DNA (Fig. 6). In addition to conventional spectroscopic techniques, a monoclonal anti-Z-DNA antibody-based enzyme-linked immunosorbent assay was developed to detect Z-DNA formation. Using the enzyme-linked immunosorbent assay technique, Z-DNA formation was also detected in (dG-dC) sequences inserted in a plasmid DNA (36). In contrast, there was no Z-DNA formation in the control plasmid, thereby showing sequence-specific interaction of polyamines with the (GC) insert. Structural specificity effect was also evident in the efficacy of three spermidine homologs to induce the Z-DNA conformation in the plasmid with insert sequences. These results indicate that spermidine and spermine are capable of provoking the left-handed Z-DNA conformation in small blocks of (dG-dC) sequences embedded in a right-handed B-DNA matrix. Because blocks of (dG-dC) sequences are found in genomic DNA, conformational alterations of these regions to the Z-DNA form may have important gene regulatory effects in the presence of polyamines.

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  • salla
    How BDNA differs from ZDNA?
    3 years ago

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