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The chiral complexes tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) (RuDIP) are shown to be specific chemical probes with which to distinguish right-and lefthanded DNA helices in solution. In spectrophotometric titrations of racemic RuDIP with both B-form calf thymus DNA and Z-form poly [d(G-C)], hypochromicity in the intense metal-to-ligand charge-transfer band is found and enhancement in luminescence is observed. The spectrophotometric assay of DNA binding to the well-resolved enantiomers of RuDIP provides a means to determine the helical conformation. Strong chiral specificity is seen in binding experiments with righthanded B-DNA and, on this basis, the absolute configurations are assigned. Although A-RuDIP can bind by intercalation into the right-handed helix, steric constraints imposed by the helix asymmetry preclude completely binding by the A enantiomer. Both isomers, however, are found to bind equally to Z-DNA. Left-handed helices that are more similar structurally to B-DNA would be predicted to display a stereospecific preference for this A isomer.The left-handed DNA helix has received considerable attention since the original crystallographic study of the Z-DNA fragment [d(CpG)]6 (1). Solution conditions that include high ionic strength (2), hydrophobic solvents (3), the presence of certain trivalent cations (4), or covalent modification with bulky alkylating agents (4-8) all facilitate the transition of a right-handed double helix into a left-handed form. This striking conformational transition was first observed for poly-[d(G-C)] (2). More recently, the alternating purine-pyrimi-, has been shown to form Z-helices as well (9, 10). Methylation of cytosine residues at carbon-5 lends stability to Z-form DNA (4, 11) and, under physiological conditions, transitions to a left-handed structure can occur to relieve the torsional strain in underwound negatively supercoiled DNA (12-14). These latter findings suggest mechanisms for left-handed DNA formation in the cell, where such structures could be important in controlling gene expression. Negatively supercoiled simian virus 40 DNA has, for example, been found to contain potentially Z-DNA-forming alternate purine-pyrimidine regions within transcriptional enhancer sequences (15).To explore any biological role for left-handed DNA, sensitive and selective probes are required. Z-DNA appears to be a strong immunogen. Anti-Z-DNA antibodies have been elic- Based on this premise, tris(phenanthroline) metal complexes appear useful in the design of probes to distinguish left-handed and right-handed DNA duplexes. The design flexibility inherent in metallointercalation reagents, in which both ligand and metal may be varied easily, makes the coordination complexes attractive probes (22-24). We have concentrated here on phenanthroline complexes of ruthenium(II) because of the high luminescence associated with their intense metal-to-ligand charge-transfer band (25,26) and because the exchange-inert character of the low-spin d6 complexes limits racemization (27)...

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The N-terminal DNA-binding domain of the GAL4 transcription factor, isolated as a proteolytic fragment of 63 amino acid residues, GAL4(63), or cloned as a 62-residue subdomain, GAL4(62*), binds 2 Cd(I1) ions. Both Cd derivatives show intense ellipticity bands associated with -S-"+ Cd charge transfer bands at 250 nm (+), 233 nm , 1987, Biochemistry 26, 6287-6292). Circular dichroism provides further evidence that the GAL4 DNA-binding domain forms a binuclear Cd cluster with the amino acid sequence ~~1 1~~~~~1 4~~~~~2 1~~~~ found in GAL4(62*). Zn2GAL4(62*) has much weaker ellipticity associated with the higher energy -S-"+ Zn charge transfer bands. Removal of the metal ions from GAL4(62*) results in substantial changes in the near UV circular dichroism due to both loss of the charge transfer bands and changes in the conformation of the peptide backbone. Binding of the UASG enhancer DNA element to either Zn or Cd GAL4(62*) alters the ellipticity of the -S-+ metal charge transfer bands suggesting that DNA binding is associated with some changes in conformation around the metal cluster.

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