Chiral probes for the handedness of DNA helices: enantiomers of tris(4,7-diphenylphenanthroline)ruthenium(II).

Abstract

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)...

Induced-fit recognition of DNA by organometallic complexes with dynamic stereogenic centers

“…In contrast to octahedral metallointercalators such as Tris-(phenanthroline)Ru(II) derivatives (20,32), [Ru(phenanthroline) 2 Cl 2 ] (33), and [Ru(bipyridine) 2 Cl 2 ] (34), which are essentially inert to racemization, have rigid frameworks, and recognize DNA mainly by shape-match (20), the {( 6 -arene)Ru(II)} complexes studied here have dynamic stereogenic centers and fluxional 6 -arene ligands. Binding of these Ru-(arene) complexes to DNA can be accompanied by configurational changes that allow recognition by an induced fit mechanism.…”

Characterization of dipyridophenazine complexes of ruthenium(II): The light switch effect as a function of nucleic acid sequence and conformation

“…Tris( 1 ,IO-phenanthroline)ruthenium(II), Ru-(phen)j2+, has been established, primarily via photophysical studies Kumar et al, 1985;Pyle et al, 1989), to bind to DNA through two noncovalent modes: (i) a groove-bound mode stabilized by hydrophobic interactions of the ligands with the minor groove of DNA and (2) intercalation in the DNA major groove (Rehmann & Barton, 1990a,b 0006-2960/92/043 1-10809$03.00/0 isomer is favored for intercalation into right-handed helices, whereas the groove-bound interaction favors the A isomer. Indeed, A-RU(DIP)~~+, the first spectroscopic probe for Z-DNA (Barton et al, 1984), was developed on the basis of the differential binding of ruthenium enantiomers to rightand left-handed helices through matching the symmetry of the metal complexes to the symmetry of the helices.Recently, a ruthenium(I1) polypyridyl derivative, Ru-(bpy)zdppz2+ (bpy = 2,2'-bipyridine; dppz = dipyrido[3,2-a:2',3'-c]phenazine), was shown to be a remarkable luminescent light switch for DNA (Friedman et al, 1990(Friedman et al, , 1991Hartshorn & Barton, 1992). The dipyridophenazine ligand, compared to the parent phenanthroline, has an extended aromatic surface area which allows for extensive intercalative stacking in DNA; dppz complexes bind avidly to DNA through intercalation [for Ru(bpy)zdppz2+ log K 1 7; for Ru(phen)32+ log K -41.…”

“…Tris( 1 ,IO-phenanthroline)ruthenium(II), Ru-(phen)j2+, has been established, primarily via photophysical studies Kumar et al, 1985;Pyle et al, 1989), to bind to DNA through two noncovalent modes: (i) a groove-bound mode stabilized by hydrophobic interactions of the ligands with the minor groove of DNA and (2) intercalation in the DNA major groove (Rehmann & Barton, 1990a,b 0006-2960/92/043 1-10809$03.00/0 isomer is favored for intercalation into right-handed helices, whereas the groove-bound interaction favors the A isomer. Indeed, A-RU(DIP)~~+, the first spectroscopic probe for Z-DNA (Barton et al, 1984), was developed on the basis of the differential binding of ruthenium enantiomers to rightand left-handed helices through matching the symmetry of the metal complexes to the symmetry of the helices.…”

Cytochemical application of tris (2,2'-bipyridine) ruthenium (II): fluorescence reaction with sulfated polyanions of mast cell granules.

“…As evaluated by spectral studies, binding of R~(phen)3~+ and Ru(DIP)s2' to DNA supports an enantiomeric stereoselectivity. The enantiomer A binds to B-DNA and the enantiomer A binds to Z-DNA (1)(2)(3)13,24).…”