Oxidation of DNA and RNA by Oxoruthenium(IV) Metallointercalators: Visualizing the Recognition Properties of Dipyridophenazine by High-Resolution Electrophoresis

Targeting structural features of viral genomes with a nano-sized supramolecular drug

RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.

Effect of metal–metal distance in Ni(ii)-based metallo-supramolecular polymers: DNA binding and cytotoxicity

Two metallo-supramolecular polymers (polyNiL1 and polyNiL2) with different metal–metal distances were synthesized via (1 : 1) complexation of the Ni salts with bis(1,10-phenanthroline)s and their DNA binding properties and cytotoxicity were revealed.

Synthesis and antimicrobial activity of polysaccharide alginate derived cationic surfactant-metal(II) complexes

New natural polysaccharide carbohydrate derivatives of sodium alginate surfactant and its cobalt, copper and zinc complexes were synthesized. Structures of the synthesized compounds are reported using FTIR, (1)H NMR and UV-vis. The critical micelle concentration (CMC) value of the alginate surfactant and its metal complexes in aqueous solution was found out from surface tension measurements. Surface tension data at different temperatures served for the evaluation of the temperature-dependent CMC and the thermodynamics of micellization (ΔGmic, ΔHmic, ΔSmic) and adsorption (ΔGads, ΔGads, ΔSads). The surface activities of the synthesized polymeric surfactant and its metal complexes were influenced by their chemical structures and the type of the transition metals. These compounds were evaluated against Gram-positive bacteria (Bacillus subtilis and Staphylococcus aureus), Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) and fungi (Candida albicans and Asperigllus niger). The antibacterial and antifungal screening tests of the alginate surfactant metal complexes have shown good results compared to its precursor alginate surfactant.

Biophysical insights into the intercalative interaction of surfactant cobalt(III) complexes of certain diimine ligands bound to yeast tRNA: Effects of hydrophobicity

The interaction of two surfactant cobalt(III) complexes, cis-[Co(ip)₂(DA)₂](ClO₄)₃ 1 and cis-[Co(dpq)₂(DA)₂](ClO₄)₃ 2 where ip=imidazo[4,5-f][1,10]phenanthroline and dpq=dipyrido[3,2-d:2'-3'-f]quinoxaline with yeast tRNA have been explored by using electronic absorption, competitive binding, electrochemical studies and viscosity measurements. The results suggest that these complexes can bind to tRNA by intercalation. The presence of hydrophobic diimine ligand and the long aliphatic double chains of these complexes facilitate its intercalative interaction with the hydrophobic interior of the tRNA. The extent of tRNA binding of complex 2 has greater affinity than that of complex containing imidazo[4,5-f][1,10]phenanthroline ligands.

Formation and nonlinear optical properties of Ag nanocrystals capped with the conjugated ligand carbazolyl styryl terpyridine

NLO (non-linear optics) properties of the optical organic molecules were significantly improved when capped with nano-Ag.

Binding of Ru(terpyridine)(pyridine)dipyridophenazine to DNA studied with polarized spectroscopy and calorimetry

Achiral Ru(tpy)(py)dppz²⁺ intercalated into DNA has similar intermolecular interactions as opposite enantiomers of its structural isomer, the “light-switch” complex Ru(bpy)₂dppz²⁺.

Nucleic acid binding study of surfactant copper(ii) complex containing dipyrido[3,2-a:2′-3′-c]phenazine ligand as an intercalator: in vitro antitumor activity of complex in human liver carcinoma (HepG2) cancer cells

A new surfactant copper(ii) complex, [Cu(dppz)₂DA](ClO₄)₂, where dppz = dipyrido[3,2-a:2′-3′-c]phenazine and DA-dodecylamine, has been synthesized and characterized by physico-chemical and spectroscopic methods.

An efficient and new protocol for phosphine-free Suzuki coupling reaction using palladium-encapsulated and air-stable MIDA boronates in an aqueous medium

A simple methodology for Suzuki–Miyaura cross-coupling reactions using microencapsulated palladium and (het)aryl MIDA boronates in water–alcohol under phosphine-free conditions was developed.

DNA/RNA binding and anticancer/antimicrobial activities of polymer-copper(II) complexes

Water soluble polymer-copper(II) complexes with various degrees of coordination in the polymer chain were synthesized and characterized by elemental analysis, IR, UV-visible and EPR spectra. The DNA/RNA binding behavior of these polymer-copper(II) complexes was examined by UV-visible absorption, emission and circular dichroism spectroscopic methods, and cyclic voltammetry techniques. The binding of the polymer-copper(II) complexes with DNA/RNA was mainly through intercalation but some amount of electrostatic interaction was also observed. This binding capacity increased with the degree of coordination of the complexes. The polymer-copper(II) complex having the highest degree of coordination was subjected to analysis of cytotoxic and antimicrobial properties. The cytotoxicity study indicated that the polymer-copper(II) complexes affected the viability of MCF-7 mammary carcinoma cells, and the cells responded to the treatment with mostly through apoptosis although a few cells succumbed to necrosis. The antimicrobial screening showed activity against some human pathogens.

Nucleic acid binding behaviors and cytotoxic properties of a Ru(II) complex

The interactions of complex [Ru(bpy)(2)(hnip)](2+) (1) {bpy = 2,2'-bipyridine, hnip = 2-(2-hydroxy-1-naphthyl)imidazo[4,5-f][1,10]phenanthroline} with calf thymus DNA and yeast tRNA were investigated by UV-vis spectroscopy, fluorescence spectroscopy, viscosity, equilibrium dialysis, and circular dichroism. In addition, the antitumor activities of complex 1 were evaluated with MTT method. These results indicate that the structures of DNA and RNA have significant effects on the binding behaviors of complex 1. Further, complex 1 demonstrates different antitumor activities against selected cancer cell lines in vitro.

Study on nucleic acid (CT-DNA and yeast tRNA) binding behaviors and cytotoxic properties of a heterodinuclear Ru(II)-Co(III) polypyridyl complex

A heterodinuclear (Ru(II), Co(III)) metal polypyridyl complex [(phen)(2)Ru(bpibH(2))Co(phen)(2)](5+) {phen = 1,10-phenanthroline, bpibH(2) = 1,4-bis([1,10]phebanthroline-[5,6-d]imidazol-2-yl)-benzene} has been designed and synthesized. The comparative study on the interactions of the Ru(II)-Co(III) complex with calf thymus DNA (CT-DNA) and yeast tRNA has been investigated by UV-visible spectroscopy, fluorescence spectroscopy, viscosity, as well as equilibrium dialysis and circular dichroism (CD). The antitumor activities of the complex have been evaluated by MTT {3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide} method and Giemsa staining experiment. These results indicate that the structures of nucleic acids have significant effects on the binding behaviors of metal complexes. Furthermore, the complex demonstrates different antitumor activity against selected tumor cell lines in vitro, and can make the cell apoptosis.

Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex

Oxidation of RNA can be effected by two different techniques: a photochemical, electron-transfer method termed "flash-quench" and direct oxidation by metal oxo complexes. The flash-quench method produces selective oxidation using a metal photosensitizer, tris(bipyridyl)ruthenium(III) trichloride (Ru(bpy)(3)(3+)), and quencher, pentaamminechlorocobalt(III) chloride (Co(NH(3))(5)Cl(2+)). We have optimized the flash-quench technique for the following RNAs: tRNA(Phe), human ferritin iron-responsive element (IRE), and a mutated human ferritin IRE. We have also employed a chemical footprinting technique involving the oxoruthenium(IV) complex (Ru(tpy)(bpy)O(2+) (tpy = 2,2',2''-terpyridine; bpy = 2,2'-bipyridine)) to oxidize guanine. Comparison of the two methods shows that the flash-quench technique provides a visualization of nucleotide accessibility for a static conformation of RNA while the Ru(tpy)(bpy)O(2+) complex selectively oxidizes labile guanines and gives a visualization of a composite of multiple conformations of the RNA structure.

Nucleic Acid (Calf Thymus-DNA, Yeast tRNA) Binding and Cytotoxic Properties of a Dinuclear (Ru,Co) Metal Polypyridyl Complex

Based on [L2Ru{DPPZ(11–11′)DPPZ}RuL2]4+ (where L = 1,10-phenanthroline or 2,2′-bipyridyl, DPPZ(11–11′)DPPZ = 11,11′-bi(dipyrido-[3,2-a:2′,3′-c]-phenazinyl)), a heterodinuclear (Ru,Co) metal polypyridyl complex [(phen)2Ru{DPPZ(11–11′)DPPZ}Co(phen)2]5+ (phen = 1,10-phenanthroline) has been designed and synthesized. A comparative study on the interaction of the complex with calf thymus DNA and yeast tRNA was investigated by UV-visible spectroscopy, fluorescence spectroscopy and viscosity measurements, as well as equilibrium dialysis and circular dichroism. The antitumour activities of the complex were evaluated by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetraazolium bromide method and Giemsa staining experiment. These results indicate that the configuration and structures of nucleic acids have significant effects on the binding behaviours of metal complexes. Furthermore, the complex shows different antitumour activities against selected tumour cell lines, and can cause cell apoptosis.

DNA interactions and photocatalytic strand cleavage by artificial nucleases based on water-soluble gold(III) porphyrins

The novel gold porphyrin complex (5,10,15-tris(N-methylpyridinium-4-yl)-20-(1-pyrenyl)-porphyrinato)gold(III) chloride, [Au(III)(TMPy3Pyr1P)]Cl4, was prepared and characterized by optical spectroscopy, high-resolution nuclear magnetic resonance (NMR), and electrospray mass spectrometry. This cationic multichromophore compound exhibits excellent water solubility and does not form aggregates under physiological conditions. Binding interactions of this complex and related model compounds with nucleic acid substrates have been studied and characterized by NMR and circular dichroism spectroscopy. The photoreactivity of [Au(III)(TMPy3Pyr1P)]Cl4 was investigated under anaerobic and aerobic conditions in the presence of an excess of purine nucleoside, guanosine, and plasmid DNA. Photocatalytic oxidative degradation of guanosine and the change from supercoiled to circular plasmid DNA upon monochromatic irradiation and polychromatic blue-light exposure with a maximum at 420 nm was explored. The potential of the novel water-soluble cationic metallointercalator complex [Au(III)(TMPy3Pyr1P)]Cl4 to serve as a catalytic photonuclease for the cleavage of DNA has been demonstrated.

Sensitive voltammetric detection of yeast RNA based on its interaction with Victoria Blue B

Voltammetric studies of the interaction of yeast RNA (y-RNA) with Victoria Blue B (VBB) are described in this paper. Furthermore, a linear sweep voltammetric method for the detection of y-RNA was established. The reaction conditions, such as acidity and amount of buffer solution, the concentration of VBB, the reaction time and temperature, etc., were carefully investigated by second order derivative linear sweep voltammetry. Under the optimal conditions, the reduction peak current of VBB at -0.75V decreased greatly after the addition of y-RNA to the solution without any shift of the reduction peak potential. Based on the decrease of the peak current, a new quantitative method for the determination of y-RNA was developed. The effects of co-existing substances on the determination were carefully investigated and three synthetic samples were determined with satisfactory results. The stoichiometry of the VBB-y-RNA complex was calculated by linear sweep voltammetry and the interaction mechanism is discussed.

2,4,6-Trisubstituted pyridines: Synthesis, topoisomerase I and II inhibitory activity, cytotoxicity, and structure–activity relationship

Designed and synthesized were a series of pyridines substituted at 2, 4, and 6 positions with various 5- or 6-memberd heteroaromatics as antitumor agents. They were evaluated their topoisomerase I and II inhibitory activities along with cytotoxicities against several human cancer cell lines. Among the prepared compounds, 10-20 showed significant topoisomerase I or II inhibitory activities, and 21-26 showed considerable cytotoxicities against several human cancer cell lines. Structure-activity relationship study indicates that 4'-pyridine at 6-position of central pyridine plays a key role in biological activity.

Marked Differences in Light-Switch Behavior of Ru(II) Complexes Possessing a Tridentate DNA Intercalating Ligand

The tridentate ligand 3-(pyrid-2'-yl)dipyrido[3,2-a:2',3'-c]phenazine (pydppz) has been prepared in two steps by elaboration of 2-(pyrid-2'-yl)-1,10-phenanthroline. Both homoleptic [Ru(pydppz)(2)](2+) and heteroleptic [Ru(tpy)(pydppz)](2+) (tpy = 2,2';6',2' '-terpyridine) complexes have been prepared and characterized by (1)H NMR. The absorption and emission spectra are consistent with low-lying MLCT excited states, which are typical of Ru(II) complexes. Femtosecond transient absorption measurements show that that the (3)MLCT excited state of the heteroleptic complex [Ru(tpy)(pydppz)](2+) (tau approximately 5 ns) is longer-lived than that of the homoleptic complex [Ru(pydppz)(2)](2+) (tau = 2.4 ns) and that these lifetimes are significantly longer than that of the (3)MLCT state of the parent complex [Ru(tpy)(2)](2+) (tau = 120 ps). These differences are explained by the lower-energy (3)MLCT excited state present in [Ru(tpy)(pydppz)](2+) and [Ru(pydppz)(2)](2+) compared to [Ru(tpy)(2)](2+), resulting in less deactivation of the former through the ligand-field state(s). DFT and TDDFT calculations are consistent with this explanation. [Ru(tpy)(pydppz)](2+) and [Ru(pydppz)(2)](2+) bind to DNA through the intercalation of the pydppz ligand; however, only the heteroleptic complex exhibits luminescence enhancement in the presence of DNA. The difference in the photophysical behavior of the complexes is explained by the inability of [Ru(pydppz)(2)](2+) to intercalate both pydppz ligands, such that one pydppz always remains exposed to the solvent. DNA photocleavage is observed for [Ru(tpy)(pydppz)](2+) in air, but not for [Ru(pydppz)(2)](2+). The DNA damage likely proceeds through the production of small amounts of (1)O(2) by the longer-lived complex. Although both complexes possess the intercalating pydppz ligand, they exhibit different photophysical properties in the presence of DNA.

Synthesis of 2,6-diaryl-substituted pyridines and their antitumor activities

For the development of novel antitumor agents, we designed and synthesized 2,6-diaryl-substituted pyridine derivatives bearing three aryl groups, which are the bioisosteres of terpyridine, and evaluated their biological activities. Most of the 18 prepared compounds showed moderate cytotoxicity against several human cancer cell lines. From the structure-activity relationships we may conclude that the number of aryl groups employed would be critical for their biological activities.