Photoreactions of ruthenium(II) and osmium(II) complexes with deoxyribonucleic acid (DNA)

Novel DNA sensor for guanine content

The bifunctional complex [Ru(TAP)(2)POQ-Nmet](2+), 1, formed with a [Ru(TAP)(2)Phen](2+) metallic unit linked to a quinoline moiety, and [Ru(TAP)(2)Phen](2+), 2, as reference, have been tested as photoprobes of DNA. Interestingly, 1 exhibits an emission enhancement of a factor of 16-17 upon binding to calf thymus DNA. Moreover, this emission is modulated by the nucleic base content of the polynucleotide. It varies by almost an order of magnitude from a polynucleotide containing 100% of G-C to a guanine-free nucleic acid where the excited-state lifetime reaches about 2 micros. The origins of these interesting properties are analyzed by comparing 1 with reference 2 in the presence of different polynucleotides.

Luminescence quenching of Ru-labeled oligonucleotides by targeted complementary strands

The yield of hole injection into guanines of different oligonucleotide duplexes by a photooxidizing tethered Ru(II) complex is examined by measuring the luminescence quenching of the excited complex. This yield is investigated as a function of the anchoring site of the complex (on a thymine nucleobase in the middle of the sequence or on the 5' terminal phosphate) and the number and position of the guanine bases as compared with the site of attachment of the Ru(II) compound. In contrast to other studies, the tethered complex, [Ru(tap)(2)(dip)](2+), is a non-intercalating compound and has been shown previously to produce an irreversible photocrosslinking between the two strands as the ultimate step of hole injection. The study of luminescence quenching of the anchored complex by emission intensity and lifetime measurements for the different duplexes indicates that a direct contact between the complex and the guanine nucleobase is needed for the electron transfer to take place. Moreover, for none of the sequences a clear contribution of a static quenching is evidenced independently of the two types of attachment of the [Ru(tap)(2)(dip)](2+) complex to the oligonucleotide. A comparison of the fastest hole-injection process by electron transfer to the excited anchored [Ru(tap)(2)(dip)](2+), with the rate of the photo-electron transfer between the same complex free in solution and guanosine-5'-monophosphate, indicates that the hole injection by the anchored complex is slower by a factor of 10 at least. A bad overlap between donor and acceptor orbitals is probably the cause of this slow rate, which could be attributed to some steric hindrance induced by the complex linker.

Synthesis of [Ru(phen)(2)dppz](2+)-tethered oligo-DNA and studies on the metallointercalation mode into the DNA duplex

To explore the binding properties of [Ru(phen)(2)dppz](2+) complex (phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine) in a sequence-specific manner in DNA duplex, it was tethered through the dppz ligand to a central position as well as both at the 3'- and 5'-ends of oligodeoxyribonucleotide (ODN). The middle [Ru(phen)(2)dppz](2+)-ODN tethered was resolved and isolated as four pure diastereomers, while the 3'- or 5'-[Ru(phen)(2)dppz](2+)-ODNs were inseparable on RP-HPLC. Thermal stability of the (Ru(2+)-ODN).DNA duplexes is found to increase considerably (DeltaT(m) = 12.8-23.4 degrees C), depending upon the site of the covalent attachment of the tethered [Ru(phen)(2)dppz](2+) complex, or the chirality of the [Ru(phen)(2)dppz](2+)-linker tethered at the middle of the ODN, compared to the unlabeled counterpart. Gross differences in CD between the [Ru(phen)(2)dppz](2+)-tethered and the native DNA duplexes showed that the global duplex conformation of the former has considerably altered from the B-type, but is still recognized by DNase I. The thermal melting studies, CD measurements, as well as DNase I digestion data, are interpreted as a result of intercalation of the dppz moiety, which is realized by threading of the Ru(phen)(2) complex part through the DNA duplex core. DNase I footprinting with four diastereomerically pure middle ([Ru(phen)(2)dppz](2+)-ODN).DNA duplexes furthermore showed that the tethered [Ru(phen)(2)dppz](2+)-linker chirality dictates the stereochemical accessibility of various phosphodiester moieties (around the intercalation site) toward the cleavage reaction by the enzyme. The diastereomerically pure ruthenium-modified duplexes, with the well-defined pi-stack, will be useful to explore stereochemistry-dependent energy- and electron-transfer chemistry to understand oxidative damage to the DNA double helix as well as the long-range energy- and electron-transfer processes with DNA as a reactant.

Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base

Fluorescently labeled oligonucleotide probes have been widely used in biotechnology, and fluorescence quenching by the interaction between the dyes and a nucleobase has been pointed out. This quenching causes big problem in analytical methods, but is useful in some other cases. Therefore, it is necessary to estimate the fluorescence quenching intensity under various conditions. We focused on the redox properties of some commercially available fluorescent dyes, and investigated dye-nucleotide interactions between a free dye and a nucleotide in aqueous solution by electrochemical and spectroscopic techniques. Our results suggested that the quenching was accompanied by photoinduced electron transfer between a thermodynamically quenchable excited dye and a specific base. Several kinds of fluorescent dyes labeled to the 5'-end of oligonucleotide C10T6 were prepared, and their quenching ratios compared upon hybridization with the complementary oligonucleotide A6G10. The quenching was completely reversible and their efficiencies depended on the attached fluorophore types. The fluorescence of 5-FAM, BODIPY FL or TAMRA-modified probe was strongly quenched by hybridization.

Ruthenium(II) complexes of 6,7-dicyanodipyridoquinoxaline: synthesis, luminescence studies, and DNA interaction

The hexaflurophosphate and chloride salts of a series of ruthenium(II) complexes incorporating a new dipyridophenazine-based ligand, dicnq (6,7-dicyanodipyrido[2,2-d:2',3'-f]quinoxaline), are synthesized in good-to-moderate yields. These mono ([Ru(phen)2(dicnq)]2+; phen = 1,10-phenanthroline), bis ([Ru(phen)(dicnq)2]2+), and tris ([Ru(dicnq)3]2+) complexes are fully characterized by elemental analysis, infrared, FAB-MS, 1H NMR, and cyclic voltammetric methods. Results of absorption titration and thermal denaturation studies reveal that these complexes are moderately strong binders of calf-thymus (CT) DNA, with their binding constants spanning the range (1-3) x 10(4) M-1. On the other hand, under the identical set of experimental conditions of light and drug dose, the DNA (pBR 322)-photocleavage abilities of these ruthenium(II) complexes follow the order [Ru(phen)2(dicnq)]2+ > [Ru(phen)(dicnq)2]2+ >> [Ru(dicnq)3]2+, an order which is the same as that observed for their MLCT emission quantum yields. Steady-state emission studies carried out in nonaqueous solvents and in aqueous media with or without DNA reveal that while [Ru(dicnq)3]2+ is totally nonemissive under these solution conditions, both [Ru(phen)2(dicnq)]2+ and [Ru(phen)(dicnq)2]2+ are luminescent and function as "molecular light switches" for DNA. Successive addition of CT DNA to buffered aqueous solutions containing the latter two complexes results in an enhancement of the emission in each case, with the enhancement factors at saturation being approximately 16 and 8 for [Ru(phen)2(dicnq)]2+ and [Ru(phen)(dicnq)2]2+, respectively. These results are discussed in light of the relationship between the structure-specific deactivations of the MLCT excited states of these metallointercalators and the characteristic features of their DNA interactions, and attempts are made to compare and contrast their properties with those of analogous dipyridophenazine-based complexes, including the ones reported in the preceding paper.

Cytochemistry of mast cells: new fluorescent methods selective for sulfated glycosaminoglycans

The development and application of simple and selective fluorescent methods for routine detection of mast cells are of considerable interest because these cells play an important role in health and disease. In the present study, aspects of staining of sulfated glycosaminoglycans with carbocyanines, aryloxazoles, and a ruthenium(II) complex are discussed. The most suitable of these compounds for visualizing mast cells in smears and tissue sections are DiOC1 (3), Q-dmPOPOP, PyPO, and Rubipy, which have been practically overlooked as cationic fluorochromes for fixed cells. Bicolour fluorescence allowing simultaneous observation of mast cells and other cell types and tissue components by application of these dyes in combination with haematoxylin and/or eosin, or by counterstaining with other fluorochromes or fluorescent complexes is particularly useful for routine histopathological studies. Simple and reliable staining procedures, bright emission, high sensitivity and stability, permanent mounting, and possibilities for combined use with other histochemical methods are the most relevant advantages of these mast cell fluorochromes.

Spectral and Structural Characterization of 5,6-Chrysenequinone Diimine Complexes of Rhodium(III): Evidence for a pH-Dependent Ligand Conformational Switch

Rhodium(III) complexes containing 9,10-phenanthrenequinone diimine (phi) ligands have been broadly applied for the construction of DNA binding and recognition molecules, and more recently, derivatives containing the 5,6-chrysenequinone diimine (chrysi) ligand have been shown specifically to recognize base mismatches in DNA. Here the structural properties of [Rh(bpy)(2)(chrysi)]Cl(3) and spectroscopic properties of derivatives are examined and compared to those of phi complexes of rhodium. Although similar in many respects, phi and chrysi complexes display distinctly different protonation behavior. The pK(a) values of chrysi complexes are as much as 1 unit lower than analogous phi compounds, and visible spectra of the chrysi complexes differ markedly from the phi counterparts in acidic but not basic solution. This protonation behavior is traced to the presence of a steric clash between a proton on the aromatic ring of the chrysi ligand and the acidic immino proton of the metal complex. In avoidance of this steric clash, a significant disruption in the planarity of the chrysi ligand is evident crystallographically in the structure of [Rh(bpy)(2)(chrysi)]Cl(3).3CH(3)CN.2H(2)O (triclinic crystal system, space group P&onemacr; (No. 2), Z = 2, a = 9.079(3) Å, b = 10.970(3) Å, c = 21.192(8) Å, alpha = 86.71(3) degrees, beta = 89.21(3) degrees, gamma = 78.58(3) degrees, V = 2065.4(12) Å(3)). Phi complexes, lacking the additional aromatic ring, require no similar distortion from ligand planarity. NMR spectra support this pH-dependent structural distortion for the chrysi complex. Rhodium complexes of chrysenequinone diimine, therefore, not only represent new DNA binding molecules targeted to mismatches but also provide an illustration of a pH "gated" ligand conformational switch.