Effect of cyclic substituents on the anti-cancer activity and DNA interaction of ruthenium(II) bis-phenanthroline dipyridoquinoline.

Ruthenium(II) complexes have emerged recently as candidates for anti-cancer therapy, where activity is related to lipohilicity, cellular localization, and specific interactions with biomolecules. In this work, two novel complexes were synthesized and are reported based on the [Ru(phen)(dipyrido[3,2-:2',3'-]quinoxaline] framework. Compared to the parent complex, annealing of cyclopenteno and cyclohexeno rings to the extended ligand substantially increased cytotoxicity towards a number of cancer cell lines, and induced apoptosis.

Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions.

Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA).

Diastereomeric Crowding Effects in the Competitive DNA Intercalation of Ru(phenanthroline)dipyridophenazine Enantiomers.

The biexponential excited-state emission decay characteristic of DNA intercalated tris-bidentate dppz-based ruthenium complexes of the general form Ru(L)dppz has previously been explained by a binding model with two distinct geometry orientations of the bound ligands, with a distinct lifetime associated with each orientation. However, it has been found that upon DNA binding of Ru(phen)dppz the fractions of short and long lifetimes are strongly dependent on environmental factors such as salt concentration and, in particular, temperature. Analyzing isothermal titration calorimetry for competitive binding of Ru(phen)dppz enantiomers to poly(dAdT), we find that a consistent binding model must assume that the short and long lifetimes states of intercalated complexes are in equilibrium and that this equilibrium is altered when neighboring bound ligands affect each other.

Self-Priming Enzymatic Fabrication of Multiply Modified DNA.

The self-priming synthesis of multiply modified DNA by the extension of repeating unit duplex "oligoseeds" provides a source of versatile DNA. Sterically-demanding nucleotides 5-Br-dUTP, 7-deaza-7-I-dATP, 6-S-dGTP, 5-I-dCTP as well as 5-(octadiynyl)-dCTP were incorporated into two extending oligoseeds; [GATC] /[GATC] and [A G] /[CT ] . The products contained modifications on one or both strands of DNA, demonstrating their recognition by the polymerase as both template (reading) and substrate (writing).

The Synthesis of Designer DNA.

The synthesis of designer DNA requires an approach where the user can determine both the sequence and the number of nucleobases. The protocol outlined here describes an enzymatic method for the synthesis of long repeat-sequence DNA. The method utilizes a PCR-based approach; starting with short oligo-seeds, c.

Duplex Healing of Selectively Thiolated Guanosine Mismatches through a Cd Chemical Stimulus.

The on-column selective conversion of guanosine to thioguanosine (tG) yields modified oligomers that exhibit destabilisation over the fully complementary duplex. Restoration to a stabilised duplex is induced through thio-directed Cd coordination; a route for healing DNA damage. Short oligomers are G-specifically thiolated through a modified on-column protocol without the need for costly thioguanosine phosphoramidites.

Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes.

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)], [poly(dA-dT)], and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled.

Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides.

The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)] and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)] is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases.

Click modification of diazido acridine intercalators: a versatile route towards decorated DNA nanostructures.

Diazido derivatives of 3,6-diamino acridine (proflavine) intercalate into DNA and undergo functionalization through click chemistry to form 1D nanostructures with redox active, conductive nanowire, and fluorescent properties. This two-step approach, intercalation followed by click modification allows for the controlled decoration of DNA nanostructures.

Enzymatic Method for the Synthesis of Long DNA Sequences with Multiple Repeat Units.

A polymerase chain reaction (PCR) derived method for preparing long DNA, consisting of multiple repeat units of one to ten base pairs, is described. Two seeding oligodeoxynucleotides, so-called oligoseeds, which encode the repeat unit and produce a duplex with 5'-overhangs, are extended using a thermostable archaeal DNA polymerase. Multiple rounds of heat-cool extension cycles, akin to PCR, rapidly elongate the oligoseed.

Sensitivity of [Ru(phen)2dppz]2+ light switch emission to ionic strength, temperature, and DNA sequence and conformation.

The luminescence of DNA-bound [Ru(phen)(2)dppz](2+) is shown to be highly sensitive to environmental conditions such as ionic strength, temperature, and the sequence and secondary structure of the nucleic acid, although not to bulky DNA substituents in the major groove. Each enantiomer has two characteristic lifetimes with any polynucleotide and their relative amplitudes vary as a function of binding ratio. For [poly(dA-dT)](2) as a model sequence, the longer lifetime for Δ-[Ru(phen)(2)dppz](2+) has been assigned to canted intercalation of the complex and the shorter lifetime is ascribed to symmetric intercalation.

Lifetime heterogeneity of DNA-bound dppz complexes originates from distinct intercalation geometries determined by complex-complex interactions.

Despite the extensive interest in structurally explaining the photophysics of DNA-bound [Ru(phen)(2)dppz](2+) and [Ru(bpy)(2)dppz](2+), the origin of the two distinct emission lifetimes of the pure enantiomers when intercalated into DNA has remained elusive. In this report, we have combined a photophysical characterization with a detailed isothermal titration calorimetry study to investigate the binding of the pure Δ and Λ enantiomers of both complexes with [poly(dAdT)](2). We find that a binding model with two different binding geometries, proposed to be symmetric and canted intercalation from the minor groove, as recently reported in high-resolution X-ray structures, is required to appropriately explain the data.

DNA sequence and ancillary ligand modulate the biexponential emission decay of intercalated [Ru(L)2dppz]2+ enantiomers.

The bi-exponential emission decay of [Ru(L)(2)dppz](2+) (L = N,N'-diimine ligand) bound to DNA has been studied as a function of polynucleotide sequence, enantiomer, and nature of L (phenanthroline vs. bipyridine). The lifetimes (τ(i)) and pre-exponential factors (α(i)) depend on all three parameters.

Influence of polystyrenesulfonate on electron transfer quenching of ruthenium trisbipyridine luminescence by viologens: non-covalent assembly and covalent tethering of the ruthenium complex.

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.

Picosecond Kerr-gated time-resolved resonance Raman spectroscopy of the [Ru(phen)(2)dppz](2+) interaction with DNA.

To investigate the basis of the 'light-switch' effect, the solvent dependence of the Kerr-gated picosecond-time resolved resonance Raman (TR(3)) spectra of [Ru(bpy)(2)dppz](2+), [Ru(phen)(2)dppz](2+), and the modified complex [Ru(phen)(2)cpdppzOMe](2+) and a dimer [mu-C4(cpdppz)(2)-(phen)(4)Ru(2)](4+) were studied. The investigation focussed on comparing the behaviour of [Ru(phen)(2)dppz](2+) in acetonitrile, ethanol, H(2)O, D(2)O, and DNA. The data are consistent with a model wherein excitation induces metal-to-ligand charge transfer (MLCT) to any of the ligands (termed the 'precursor' state) which, by interligand electron transfer (ILET), produces an excited state localised on the dppz ligand, MLCT(1).