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The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)]2, [poly(dA-dT)]2, and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of agg...

This review primarily covers studies of ruthenium(II) complexes with the dppz (dipyrido[2,3-a:3',2'-c]phenazine) ligand; in solution, in polymers and surfactant/lipid media, and when bound to DNA. Related studies with other transition metals, and with extended ligands that can form bimetallic as well as monometallic complexes are discussed. The review focuses on photophysics of these complexes with particular attention devoted to the nature of the excited states that give rise to emission, their dependence on solvent environment, and the behavior of the complexes as luminescent probes for DNA.

Phosphorylation of β-cyclodextrin enhances binding with Ru(II)polypyridyl complexes, and promotes selectivity based on chirality and ligand hydrophobicity. For [Ru(phen)2dppz](2+), inclusion of dppz results in a dramatic increase in luminescence with multiple lifetimes. The sensitive response of photophysics to the environment reveals nanoscale variation of polarity.

Picosecond time-resolved resonance Raman (picosecond-TR3) spectroscopy has been used to conduct an extensive photophysical characterization of the "light- switch" complex [Ru(phen)(2)dppz](2+) as a function of environment, in which studies have been carried out in aqueous and nonaqueous media and in DNA. The results are considered in rotation to a previous report describing "environment-sensitive" lowest triplet MLCT states. Vibrational marker features and enhancement patterns were used to determine the rapid progression (< 20 ps) between two triplet MLCT states in aqueous environment, followed by subnanosecond, nonradiative deactivation to the ground state. In nonaqueous environment, the long-lived, emissive triplet MLCT state is spectrally identified as the short-lived first triplet MLCT state observed in water, in agreement with the earlier proposed mechanism. The present data are shown to correlate well with previous nanosecond RR findings for the complex in each environment. Interestingly, a "precursor state" has been identified upon excitation in both nonaqueous solvent and in DNA, which precedes the triplet MLCT state, and the lifetime of which appears to be environment dependent. Observation of this state is discussed in relation to other recent femtosecond spectroscopic studies on this complex.

The possibility that the stacked DNA bases can mediate vectorial electron transfer has been examined using two different approaches. Experiments on photoinduced electron transfer with intercalated donors and acceptors (either randomly bound or linked dyads of ruthenium complex and viologen) indicate that while DNA may be a better medium than acetonitrile for electron transfer over short distances (2-3-base pair, equivalent to 10-14Å centre-to-centre separation), it is a poor medium for transport over larger separations. Attempts to measure conductivity of individual DNA molecules using scanning tunneling microscopy to image mixed monolayers of mercaptohexanol (MCH) and 30-mer or 10-mer DNAs with alkanethiol linkers also indicate that DNA in its native state is a poor conductor. AFM images of the DNA/MCH mixed monolayers show that the DNA molecules extend vertically upward from the surface in such surface architectures.

The sub-picosecond deactivation of the thionine singlet state by guanine-containing polynucleotides or mononucleotides has been measured by femtosecond transient absorption spectroscopy. The thionine singlet state was also quenched, although less efficiently, by adenine nucleotides. In contrast, the lifetime of the methylene blue singlet state is only slightly affected by adenine-containing species, although it was rapidly quenched by guanine. A strong correlation was observed between the rates of singlet state deactivation and the Δ G ° values for electron transfer in the dye/nucleotide base systems, although with the thionine/guanine systems no electron transfer products were detected.

The light-induced reactions of methylene blue and related phenothiazinium dyes with biological substrates are described. The properties of the excited states of the dyes, their reactions with nucleic acids and their photosensitised chemical modifications of nucleic acid bases are examined. Reports on phenothiazinium dye-induced damage to proteins, lipids, biological membranes, organelles, viruses, bacteria, mammalian cells and carcinomas are reviewed.

The photobleaching of the cyanine dyes YO and YOYO has been investigated for both free and DNA-bound dyes, using absorption and fluorescence spectroscopy coupled with fluorescence microscopy. For the free dyes, the nature of the reactive species involved in the photodegradation process is different for the monomer and the dimer, as shown by scavenger studies. For DNA-bound dyes, photoinduced fading of the visible absorption band occurs by different pathways depending on the drug binding mode and can be attenuated by appropriate scavengers. However, none of these scavengers were found to have any significant effect on the photobleaching of dye fluorescence. It appears that the reduction of fluorescence intensity comes from a quenching of the dye fluorescence by modified DNA bases, possibly 8-oxo-7,8-dihydro-2‘-deoxyguanosine.

A new copolymer (RuB-PSS) of ruthenium(II)bis-(2,2'-bipyridine)(4-vinyl 2,2'-bipyridine) and styrene sulfonate was prepared which tethers the ruthenium chromophore directly to the polymer backbone. The photophysical properties of the copolymer, and its luminescence quenching by viologens, were compared with those of ruthenium(II)tris-bipyridine, [Ru(bpy)(3)](2+), bound non-covalently to polystyrenesulfonate (PSS) via hydrophobic and electrostatic interactions. Enhancement of ruthenium polypyridyl complex luminescence in both systems is due to decreased rates of non-radiative decay when removed from bulk water as well as reduced oxygen quenching. Molecular dynamics simulations show an open PSS chain conformation with induction of local curvature around the ruthenium centres. Hence, the complexes remain exposed to water, albeit less so than in bulk solution, as evidenced by low enhancement of bound [Ru(phen)(2)dppz](2+) emission. Quenching by O(2) is hindered for both systems due to combined polarity, ionic strength, and viscosimetric effects that influence local concentrations and diffusion of reactants. Electron transfer quenching of the Ru centre by zwitterionic propyl viologen sulfonate (PVS(0)) and cationic methyl viologen (MV(2+)) is enhanced for [Ru(bpy)(3)](2+)/PSS, but retarded for RuB-PSS, despite the attraction of the quenchers for PSS. PSS binding hinders separation of the electron transfer products relative to aqueous solution, excepting an increase for RuB-PSS/PVS(0). We conclude that anionic hydrophobic polymers such as PSS can differentially influence forward- and reverse- electron transfer reactions depending on the charge and hydrophobicity of the reactants. In the context of small molecule binding, we find that PSS provides a tenable model for DNA.

Δ- and Λ-[Ru(dpphen)3]2+ (dpphen = 4,7-diphenyl-1,10-phenanthroline) bind non-intercalatively to B-form DNA and, unlike other octahedral metal complexes, show insignificant enantioselectivity in their interaction.