Zinc destabilizes DNA Watson-Crick pairs at AGCT

Zn2+ blocks annealing of complementary single-stranded DNA in a sequence-selective manner

Zinc is the second most abundant trace element essential for all living organisms. In human body, 30–40% of the total zinc ion (Zn²⁺) is localized in the nucleus. Intranuclear free Zn²⁺ sparks caused by reactive oxygen species have been observed in eukaryotic cells, but question if these free Zn²⁺ outrages could have affected annealing of complementary single-stranded (ss) DNA, a crucial step in DNA synthesis, repair and recombination, has never been raised. Here the author reports that Zn²⁺ blocks annealing of complementary ssDNA in a sequence-selective manner under near-physiological conditions as demonstrated in vitro using a low-temperature EDTA-free agarose gel electrophoresis (LTEAGE) procedure. Specifically, it is shown that Zn²⁺ does not block annealing of repetitive DNA sequences lacking CG/GC sites that are the major components of junk DNA. It is also demonstrated that Zn²⁺ blocks end-joining of double-stranded (ds) DNA fragments with 3′ overhangs mimicking double-strand breaks, and prevents renaturation of long stretches (>1 kb) of denatured dsDNA, in which Zn²⁺-tolerant intronic DNA provides annealing protection on otherwise Zn²⁺-sensitive coding DNA. These findings raise a challenging hypothesis that Zn²⁺-ssDNA interaction might be among natural forces driving eukaryotic genomes to maintain the Zn²⁺-tolerant repetitive DNA for adapting to the Zn²⁺-rich nucleus.

The binding of zinc (II) to a double-stranded oligodeoxyribonucleotide. A voltammetric study

Binding of zinc to a 19 mer double-stranded oligodeoxyribonucleotide was investigated by anodic stripping voltammetry and cyclic voltammetry in order to understand the roles of zinc in DNA cleavage catalyzed by mung bean nuclease. These methods rely on the direct monitoring of zinc oxidation current in the absence and in the presence of the oligo. Zinc titration curves with the ds-oligodeoxyribonucleotide were obtained in concentrations ranging from 3.62 x 10(-9) to 3.62 x 10(-8) M and 4.06 x 10(-10) to 5.25 x 10(-9) M. The acquired data were used to determine the dissociation constant, stoichiometry and zinc binding sites of the complex and to understand the specific changes of ds-oligodeoxyribonucleotide secondary structure by zinc binding. The oxidation-reduction process of zinc was also investigated by cyclic voltammetry through I (oxidation current) versus v(1/2) (square root of scan rate) curves in the absence and in the presence of the double-stranded oligodeoxyribonucleotide.

Simultaneous N7,O6-binding of guanine to two zinc centers and its possible biological significance

The reaction of ZnCl(2) with 9-ethylguanine (9-EtGH) produced a novel dinuclear Zn(II) complex, [Zn(2)Cl(4)(H(2)O)(mu-9-EtGH-N7,O6)(9-EtGH-N7), 1. The X-ray structure analysis (monoclinic, P2(1) (No. 4), a = 11.0636(6) A, b = 6.6546(4) A, c = 15.9630(9) A, beta = 101.069(1) degrees, V = 1153.4(1) A(3), Z = 2) revealed that one of the tetrahedrally coordinated Zn(II) atoms binds to the N7 site of 9-EtGH and to the exocyclic O6 atom of another 9-EtGH molecule. The remaining Zn(II) atom binds to the N7 site of the second 9-EtGH moiety.

Millimolar concentrations of zinc and other metal cations cause sedimentation of DNA

We demonstrate that DNA sediments in the presence of millimolar concentrations of zinc or related metal cations and that EDTA entirely dissolves the sediment. The sedimentation is promoted by alkaline pH but the pH dependence is abolished by submillimolar concentrations of phosphate anions. We suspect that the metal cations generate sedimenting particles of insoluble hydroxides or phosphates for which DNA has a strong affinity. The events involved in DNA-metal phosphate co-sedimentation are similar to the processes that enable calcium phosphate-assisted transfection. Hence, work with even submillimolar concentrations of zinc and most other metal cations, which many DNA-binding proteins need for their activities, requires care to avoid the sedimentation of DNA. Literature reporting about zinc effects on DNA is discussed from the point of view of the present results.

Kinetic and structural probing of the precleavage synaptic complex (type 0) formed during phage Mu transposition. Action of metal ions and reagents specific to single-stranded DNA

In an earlier kinetic study (Wang, Z., and Harshey, R. M. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 699-703), we showed that supercoiling free energy was utilized during Mu transposition to lower the activation barrier of some rate-limiting step in the formation of the cleaved Mu end synaptic complex (type I complex). We report here results from kinetic studies on the assembled but uncleaved synaptic complex (type 0). Based on the estimated rate constants for the formation of type 0 and type I complexes, as well as their temperature and superhelicity dependence, we infer that the type 0 complex is an authentic intermediate in the pathway to Mu end cleavage. Our results are consistent with type 0 production being the rate-limiting step in the overall type I reaction. The conversion of type 0 to type I complex is a fast reaction, does not show strong temperature dependence, and is apparently independent of substrate superhelicity. We have explored the DNA structure within the type 0 complex using chemical and enzymatic probes. The observed susceptibility of DNA outside the Mu ends to single-strand-specific reagents suggests that a helix opening event is associated with type 0 formation. This structural perturbation could account, at least partly, for the high activation barrier to the reaction. There is a close correlation between the appearance of single strandedness near the Mu ends and the superhelicity of the DNA substrate. It is possible that supercoiling energy is utilized in effecting specific conformational transitions within DNA. We have found that Zn2+ and Co2+ ions, like Mg2+ and Mn2+ ions, can efficiently cleave the type 0 complex. However, unlike Mg2+ and Mn2+ ions, Zn2+ and Co2+ ions cannot support assembly of type 0. We discuss the implications of our findings for the mechanism of Mu transposition.

Inhibition of transcription factor IIIA-DNA interactions by xenobiotic metal ions

Transcription factor IIIA (TFIIIA), a cysteine-rich regulatory protein, is the prototype for the largest known superfamily of eukaryotic transcription factors. Members of the TFIIIA superfamily contain Cys2His2 zinc finger domains responsible for nucleic acid binding. Xenobiotic metal ions, which lack known biological function, were previously used as probes for the structure and function of steroid hormone receptors which contain Cys2Cys2 zinc finger domains. Structural alterations in cysteine-rich regulatory proteins by such ions in vivo might potentiate carcinogenesis and other disease processes. In the present study cadmium and other xenobiotic metal ions were used to probe the structure and function of TFIIIA. The specific interaction of TFIIIA with the internal control region (ICR) of the 5S RNA gene, as assayed by DNase I protection, was inhibited by Cd2+ ion concentrations of > or = 0.1 microM. Aluminum ions were also found to inhibit the TFIIIA-5S RNA gene interaction, albeit at higher concentrations (> or = 5 microM). Inhibition by either metal ion was not readily reversible. Other xenobiotic metal ions, such as mercury or cesium, were not found to be inhibitory under these conditions. None of these ions at the concentrations used in this study affected the ability of DNase I to digest DNA or restriction enzymes to specifically cleave DNA. Preincubation of TFIIIA bound to 5S RNA with either Cd2+ or Al3+ resulted in subsequent DNA binding upon dilution and RNA removal, whereas preincubation of free TFIIIA with the metal ions resulted in inhibition of subsequent DNA binding. Because 5S rRNA also binds the TFIIIA zinc finger domains, these results indicate that the 5S RNA bound to TFIIIA protects the protein from metal inhibition and implicates the zinc fingers in the inhibition mechanism. The nature of the footprint inhibition indicates that the N-terminal fingers of TFIIIA are affected by the metal ions. Cd2+ and Al3+ ions also inhibited the ability of TFIIIA to bind complementary single-stranded DNA and promote renaturation, as measured by Tris-phosphate agarose gel electrophoresis. This gel assay is sensitive to DNA conformation and Al3+ ions were found to alter the conformation of single- and double-stranded DNA in this assay. The inhibition of TFIIIA function in vitro by xenobiotic metals offers new insights into the structure and function of TFIIIA and TFIIIA-type zinc finger proteins. Inhibition by Cd2+ occurs at much lower concentrations than previously observed with steroid hormone receptors and suggests that Cys2His2 zinc finger proteins may be especially sensitive to such agents in vivo.