DNA binding and gel electrophoresis studies of a new silver(I) complex containing 2,9-dimethyl-1,10-phenanthroline ligands

The silver(I) complex, [Ag(2,9-dimethyl-1,10-phenanthroline)(2)](NO(3)) · H(2)O, has been synthesized and characterized by physicochemical and spectroscopic methods. The binding interactions of this complex with calf thymus DNA (CT-DNA) were investigated using emission, absorption, circular dichroism, viscosity measurements, and gel electrophoresis studies. The calculated binding constant, K(b), obtained from UV-vis absorption studies was 5.3 ± 0.2 × 10(4) M(-1). In fluorimetric studies, the enthalpy and entropy of the reaction between the complex and CT-DNA showed hydrophobic interaction. In addition, in the circular dichroism spectrum, silver(I) complex induces a B → A structural transition of CT-DNA. Gel electrophoresis studies demonstrated that this complex has ability to cleave the supercoiled plasmid DNA. All these results suggest that the complex interacts with CT-DNA via partial intercalative mode of binding.     

Crystal structure and nuclease activity of mono(1,10-phenanthroline) copper complex

The hydroxo-bridged dinuclear copper (II)/phen complex [Cu(2)(phen)(2)(OH)(2)(H(2)O)(2)][Cu(2)(phen)(2)(OH)(2)Cl(2)]Cl(2).6H(2)O (phen=1,10-phenanthroline) has been prepared and characterized by single crystal X-ray diffraction. The coordinated area of the complex shows two distorted [CuN(2)O(2)O(w)] and [CuN(2)O(2)Cl] square-pyramidal and one strictly planar configuration CuO(2)Cu involving two O atoms of hydroxo-bridged, Cu(2+) cations, N atoms of two phen ligands and disorder solvate water and chlorine anions. In the presence of H(2)O(2), the complex of mono(1,10-phenanthroline)copper exhibits higher activity as a nuclease than bis(1,10-phenanthroline)copper.     

DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline

Absorption spectroscopy and circular dichroism (CD) have been used to characterize the DNA binding of [Fe(phen)3]2+, [Fe(phen)2(DIP)]2+ and [Fe(phen)(DIP)2]2+ where phen and DIP stand for 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline, respectively. Both [Fe(phen)3]2+ and [Fe(phen)2(DIP)]2+ bind weakly to calf thymus DNA (CT-DNA) in an electrostatic mode, while [Fe(phen)(DIP)2]2+ binds more strongly to CT-DNA, possibly in an intercalation mode. The hypochromicity, red shift and Kb increase in the order [Fe(phen)3]2+ < [Fe(phen)2(DIP)]2+ < [Fe(phen)(DIP)2]2+ in accordance with the increase in size and hydrophobicity of the iron(II) complexes. The thermodynamic parameters obtained suggest that the DNA binding of both [Fe(phen)3]2+ and [Fe(phen)2(DIP)]2+ is entropically driven, while that of [Fe(phen)(DIP)2]2+ is enthalpically driven. A strong CD spectrum in the UV and visible region develops upon addition of CT-DNA into the racemate solution of each iron(II) complex (Pfeiffer effect). This has revealed that a shift in diastereomeric inversion equilibrium takes place in the solution to yield an excess of one of the DNA-complex diastereomers. The striking resemblance of the CD spectral profiles to those of the pure delta-enantiomer indicates that the delta-enantiomer of the iron(II) complexes is preferentially bound to CT-DNA. The mechanism of the development of Pfeiffer CD is proposed on the basis of kinetic studies on the DNA binding of the racemic iron(II) complexes.     

DNA binding of iron(II) complexes with 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline: salt effect,ligand substituent effect,base pair specificity and binding strength

The DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline(phen) and 4,7-diphenyl-1,10-phenanthroline(dip), [Fe(phen)(3)](2+), [Fe(phen)(2)(dip)](2+) and [Fe(phen)(dip)(2)](2+) has been characterized by spectrophotometric titration and melting temperature measurements. The salt concentration dependence of the binding constant has allowed us to dissect the DNA-binding constant and free energy change of each iron(II) complex into the nonelectrostatic and polyelectrolyte contributions. A comparison of the nonelectrostatic components in the binding free energy changes among iron(II) complexes has made it possible to rigorously evaluate the contribution of the ligand substituents to the DNA-binding event. The peripheral substitution of phen by two phenyl groups increases the nonelectrostatic binding constant of the iron(II) complex more than 20 times, which is equivalent to approximately 7.5 kJ mol(-1) of more favorable contribution to the DNA binding. In general, the iron(II) complexes studied have higher affinity towards the more facile A-T sequence than the G-C sequence. This preferential binding may be attributed to the steric effect induced by the ancillary part of the ligands in the course of DNA binding. The binding of disubstituted iron(II) complex to DNA is quite strong as reflected in the modest increase in the denaturation temperature (T(m)) of double helical DNA upon the interaction with the iron(II) complex.     

DNA interaction studies of a platinum(II) complex containing L-histidine and 1,10-phenanthroline ligands

The aim of this study was developing coordination complexes that can be used as inorganic medicinal agents. The water soluble [Pt(phen)(His)]NO(3)·3H(2)O complex in which phen=1,10-phenantheroline and His=L-histidine was synthesized and characterized using physicochemical methods. Binding interaction of this complex with calf thymus (CT) DNA was investigated by emission, absorption, circular dichroism, and viscosity measurement techniques. Upon addition of CT-DNA, changes were observed in the characteristic ultraviolet-visible (UV-Vis) bands (hypochromism) of the complex. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant, K(b), was 8 ± 0.2 × 10(4) M(-1). In addition, circular dichroism (CD) study showed that the phenanthroline ligand was inserted between the base pair stack of the double-helical structure of DNA. Also, the fluorescence spectral characteristics showed an increase in fluorescence intensity of the platinum complex in the presence of increasing amounts of DNA solution. The experimental results showed that the platinum complex binds to DNA via intercalative and hydrogen bonding mode.     

Noncovalent DNA binding of bis(1,10-phenanthroline)copper(I) and related compounds

The noncovalent DNA binding of the bis(1,10-phenanthroline)copper(I) complex [(Phen)2CuI] was examined under anaerobic conditions by absorption and circular dichroism spectroscopy, and viscometry, as a function of phenanthroline concentration. Analyses according to the McGhee-von Hippel method indicated that binding exhibited both neighbor-exclusion and positive cooperativity effects, with a neighbor-exclusion parameter n approximately 2 and a cooperativity parameter omega approximately 4. The association constant for (Phen)2CuI binding decreased with increasing concentration of phenanthroline in excess over that required to stoichiometrically generate (Phen)2CuI, indicating that free phenanthroline was a weak competitive inhibitor of (Phen)2CuI binding. The maximal association constant for DNA binding of (Phen)2CuI in 0.2 M NaCl and 9.8% ethanol, extrapolated to zero concentration of excess phenanthroline, was 4.7 x 10(4) M-1 (DNA base pairs). The magnitude of the neighbor-exclusion parameter, the changes in spectral properties of (Phen)2CuI induced by DNA binding, and the increase in DNA solution viscosity upon (Phen)2CuI addition are consistent with a model for DNA binding by (Phen)2CuI involving partial intercalation of one phenanthroline ring of the complex between DNA base pairs in the minor groove as suggested previously [Veal & Rill (1989) Biochemistry 28, 3243-3250]. Viscosity measurements indicated that the mono(phenanthroline)copper(I) complex also binds to DNA by intercalation; however, no spectroscopic or viscometric evidence was found for DNA binding of free phenanthroline or the bis(2,9-dimethyl-1,10-phenanthroline)copper(I) complex. DNA binding of free phenanthroline may be cooperative and induced by prior binding of (Phen)2CuI.     

Studies of sequence-specific DNA binding, DNA cleavage, and topoisomerase I inhibition by the dimeric chromomycin A3 complexed with Fe(II)

Chromomycin A3 (Chro) has been evidenced to exhibit much higher binding affinity toward Fe(II) by forming a highly stable 2:1 drug/metal complex, compared to its structural analogue, mithramycin (Mith). Different properties of the [(Chro)2-Fe(II)] complex acting on DNA, such as sequence specificity, DNA cleavage, and topoisomerase I (TopI) inhibition were studied. Kinetic analyses of surface plasmon resonance showed that the affinity of the [(Chro)2-Fe(II)] complex upon binding to hairpin DNA duplexes containing various tetranucleotide sequences follows the order: GGCC > CGCG > CCGG approximately GCGC > AGCT > ACGT > TGCA > TCGA. According to circular dichroism (CD) studies, most hairpin DNA duplexes appeared to retain their B-type conformations in the presence of the [(Chro)2-Fe(II)] complex, except the duplex containing the GGCC sequence, which exhibited the features of both A- and B-type DNA. In DNA-cleavage assays, the [(Chro) 2-Fe(II)] complex was shown to cause single-stranded cleavage of plasmid DNA because of a Fenton-type reaction. DNA cleavage activity of the [(Chro) 2-Fe(II)] complex was increased at low pH. Moreover, the complex was capable of inhibiting TopI activity. The [(Chro)2-Fe(II)] complex exhibited higher cytotoxicity than the [(Mith) 2-Fe(II)] complex in several cancer cell lines, most likely owing to its more stable dimeric structure and higher DNA-binding affinity. Our results provide significant evidence that the [(Chro)2-Fe(II)] complex could be promising in terms of its biological applications in the future.     

Synthesis, characterization, and DNA binding studies of some mixed-ligand platinum(II) complexes of 1,10-phenanthroline and amino acids

A series of complexes of the type [Pt(phen)(AA)]+ (where AA is the anion of glycine, L-alanine, L-leucine, L-phenylalanine, L-tyrosine, or L-tryptophan) has been synthesized. These complexes have been characterized by electronic absorption, infrared, and 1H NMR spectroscopy. The interaction of these complexes with calf thymus DNA has been studied using fluorescence spectroscopy. They inhibit the intercalation of ethidium bromide in DNA by intercalative binding at low concentrations and show nonintercalative binding at higher concentrations.     

Oxidative DNA damage of mixed copper(II) complexes with sulfonamides and 1,10-phenanthroline. Crystal structure of [Cu(N-quinolin-8-yl-p-toluenesulfonamidate)2(1,10-phenanthroline)

Mixed coordination compounds of Cu(II) with sulfonamides and 1,10-phenanthroline as ligands have been prepared and characterised. Single crystal structural determination of the complex [Cu(N-quinolin-8-yl-p-toluenesulfonamidate)(2)(phen)] shows Cu(II) ions are located in a highly distorted octahedral environment, probably as a consequence of the Jahn-Teller effect. The FT-IR and electronic paramagnetic resonance (EPR) spectra are also discussed. The mixed complexes prepared undergo an extensive DNA cleavage in the presence of ascorbate and hydrogen peroxide. Two of the complexes have higher nucleolytic efficiency than the bis(o-phenanthroline)copper(II) complex.     

Synthesis, crystal structure, electronic structure, bonding, photoluminescence and spectroscopic property investigations of a mononuclear 1,10-phenanthroline and 5-bromo-salicylate ternary indium(III) complex

The synthesis, X-ray structure, electronic structure, bonding, photoluminescence, spectroscopic property and characterization of an indium(III) complex, [In(Hbsac)₃(phen)] (1) (H₂bsac = 5-bromo-salicylic acid, and phen = 1,10-phenanthroline) are presented. Complex 1 is octacoordinate and carboxylate chelating, being novel and rarely reported for main group complexes. The electronic structure, bonding and the charge transfer properties of light excitation and light emission are discussed in detail using first-principles theory, including partial density of states (PDOSs), crystal orbital overlap population (COOP), the density functional theory (DFT/TDDFT) analysis schemes. The charge transfer is mainly π → π^∗ intraligand charge transfer transition (ILCT) for excitation, and π → π^∗ ligand-to-ligand charge transfer transition (LL′CT) for emission in nature.     

Mechanism of ATP inhibition of mammalian type I DNA topoisomerase: DNA binding, cleavage, and rejoining are insensitive to ATP

A general, unrefined mechanism of type I DNA topoisomerase action involves several steps including DNA binding, single-strand scission, strand passage resealing, and, possibly, readoption of an active enzyme conformation. None of these steps requires an energy cofactor; however, we have shown previously that several mammalian type I topoisomerases are, in fact, inhibited by ATP. In this study, we wanted to examine which steps in the gross topoisomerase mechanism were sensitive or insensitive to ATP. Nitrocellulose filter binding experiments showed that ATP did not interfere with the binding of DNA by the enzyme and that ATP binding by topoisomerase was 5-fold greater in the presence of DNA than in its absence. Agarose gel electrophoresis in the presence or absence of ethidium bromide indicated that resealing was unaffected by added ATP. The addition of the adenine nucleotide did not alter the pattern of camptothecin-stimulated cleavage of DNA, indicating that strand scission was not the point of inhibition. To test whether strand passage or the readoption of an active conformation was an inhibited step, we used a unique DNA topoisomer as substrate. The results argued against readoption of an active enzyme conformation as an ATP-sensitive process.     

Synthesis,cytotoxicity, DNA binding and topoisomerase II inhibition of cassiarin A derivatives

Four series of cassiarin A derivatives with alkanoyl (3a–3d), aroyl (4a–4d), hydroxy/amino-substituted ethylene glycol (5a–5c) and selenium-containing (6a) side chains were synthesized. Their antitumor activities were evaluated against BT474, CHAGO, HepG2, KATO-III, SW620 and CaSki cancer cell lines. Preliminary results demonstrated that 5b had moderate activities against HepG2 and KATO-III cell lines, while 5c showed moderate to high cytotoxicity against most tested cell lines. In addition, 6a exhibited moderate cytotoxicity against cervical cells, CaSki. DNA-binding and ethidium bromide displacement experiments suggested that 5c and 5b binds to DNA via an intercalative mode, whereas 6a did not. However, the selenium-containing cassiarin A derivative 6a inhibited topoisomerase II with more than 95% inhibition at the concentration of 50 μM. These cassiarin A derivatives showed lower toxicity to normal cells, WI-38 than amonafide therefore they are potential lead compounds to be further developed as new anticancer agents.     

An intercalative and minor groove binding model for the DNA cleavage reagent, copper(I) (1,10-phenanthroline)2

On account of the stereochemical structure and interaction characteristics of the DNA cleavage reagent copper(I) (1,10-phenanthroline)2, both intercalative and minor groove binding modes to B-DNA could be expected to occur. In the proposed model, the suitable dihedral angle between phenanthrolines allows that one of the two planar ligands partially intercalates between base pairs, and meanwhile the other ligand locates along the minor groove.     

Binding analysis of ytterbium(III) complex containing 1,10-phenanthroline with DNA and its antimicrobial activity

To evaluate the biological preference of [Yb(phen)₂(OH₂)Cl₃](H₂O)₂ (phen is 1,10-phenanthroline) for DNA, interaction of Yb(III) complex with DNA in Tris–HCl buffer is studied by various biophysical and spectroscopic techniques which reveal that the complex binds to DNA. The results of fluorescence titration reveal that [Yb(phen)₂(OH₂)Cl₃](H₂O)₂ has strongly quenched in the presence of DNA. The binding site number n, apparent binding constant K _b, and the Stern–Volmer quenching constant K _SV are determined. ΔH ⁰, ΔS ⁰, and ΔG ⁰ are obtained based on the quenching constants and thermodynamic theory (ΔH ⁰?>?0, ΔS ⁰?>?0, and ΔG ⁰?<?0). The experimental results show that the Yb(III) complex binds to DNA by non-intercalative mode. Groove binding is the preferred mode of interaction for [Yb(phen)₂(OH₂)Cl₃](H₂O)₂ to DNA. The DNA cleavage results show that in the absence of any reducing agent, Yb(III) complex can cleave DNA. The antimicrobial screening tests are also recorded and give good results in the presence of Yb(III) complex.     

Interactions of 1,10-phenanthroline and its copper complex with Ehrlich cells.

Mechanistic details of the interaction of 1,10-phenanthroline and its copper complex with Ehrlich ascites tumor cells were examined, using inhibition of cell proliferation, DNA breakage, and increased membrane permeability as indices of cellular damage. The metal chelating agent, 1,10-phenanthroline (OP), the 1:0.5 complex of 1,10-phenanthroline and CuCl2 [(OP)2Cu], and CuCl2 inhibited growth of Ehrlich ascites tumor cell monolayers during 48-h treatments by 50% at about 3.5, 2, and 70 nmol/10(5) cells/mL, respectively. (OP)2Cu at 10 nmol/10(5) cells also enhanced uptake of trypan blue dye during 6 h of treatment, while dye uptake in OP- and CuCl2-treated cells remained similar to controls. DNA breakage, measured by DNA alkaline elution, was produced during 1-h treatments with (OP)2Cu at drug/cell ratios similar to those producing growth inhibition. Copper uptake was similar for both (OP)2Cu and CuCl2. Electron spin resonance (ESR) spectroscopy suggested that cellular ligands bind copper added as (OP)2Cu or CuCl2 and then undergo time-dependent reductions of Cu(II) to Cu(I) for both forms. Inhibition of (OP)2Cu-induced single-strand scission and trypan blue uptake by scavengers of activated oxygen is consistent with participation of superoxide and H2O2 in both processes. In contrast, superoxide dismutase (SOD) did not reduce the magnitude of the fraction of cellular DNA appearing in lysis fractions prior to alkaline elution of (OP)2Cu-treated cells. Dimethyl sulfoxide (DMSO) inhibited uptake of trypan blue dye but did not inhibit DNA strand scission produced by (OP)2Cu. Thus, multiple mechanisms for generation of oxidative damage occur in (OP)2Cu-treated cells. Growth inhibition produced by OP or (OP)2Cu, as well as the low levels of strand scission produced by OP, was not reversed by scavengers.     

Action models for the antitumor drug camptothecin: formation of alkali-labile complex with DNA and inhibition of human DNA topoisomerase I

The antitumor activity of camptothecin (CPT) and its derivatives, including water-soluble topotecan (TPT), is determined by their ability to inhibit human DNA topoisomerase I (top 1). On the other hand, TPT has been recently shown to bind to DNA. The proposed models are based on a two-step mechanism of TPT (CPT) dimer interaction with two spatially close DNA duplexes. At the first step, the CPT lactone form binds to DNA (Streltsov et al., Mol. Biol. vol. 36, no. 5 (2002)) through hydrogen bonding of its C16a carbonyl with the guanine 2-amino group. At the second step, CPT is converted to the carboxylate form. In the absence of top 1, the C17 hydroxyl of CPT is involved in ester exchange (nicking of the DNA sugar-phosphate backbone followed by covalent joining of free phosphate to C17) whereas its C20 carboxyl forms two hydrogen bonds with the same guanine nucleotide at the opposite end of the broken DNA backbone. As a result, CPT binds to both ends of the broken DNA. The resulting CPT-DNA complex is alkali-labile. In the presence of top 1, after CPT conversion to the carboxylate form and DNA nicking, the C17 hydroxyl makes a branching hydrogen bond with N1 and N3 of guanine while the C20 carboxyl makes two hydrogen bonds with the NH of Tyr723 and N(delta2)H(2) of Asp722. Owing to this, rotation of one end of the broken sugar-phosphate backbone about the other becomes impossible; hence the CPT inhibitory effect on top 1. The proposed models are consistent with the current body of experimental data.     

Molecular determinants of site-specific inhibition of human DNA topoisomerase I by fagaronine and ethoxidine. Relation to DNA binding

DNA topoisomerase (top) I inhibition activity of the natural alkaloid fagaronine (NSC157995) and its new synthetic derivative ethoxidine (12-ethoxy-benzo[c]phenanthridine) has been correlated with their molecular interactions and sequence specificity within the DNA complexes. Flow linear dichroism shows that ethoxidine exhibits the same inhibition of DNA relaxation as fagaronine at the 10-fold lower concentration. The patterns of DNA cleavage by top I show linear enhancement of CPT-dependent sites at the 0.016-50 microM concentrations of fagaronine, whereas ethoxidine suppress both top I-specific and CPT-dependent sites. Suppression of top I-mediated cleavage by ethoxidine is found to be specific for the sites, including strand cut between A and T. Fagaronine and ethoxidine are DNA major groove intercalators. Ethoxidine intercalates DNA in A-T sequences and its 12-ethoxy-moiety (absent in fagaronine) extends into the DNA minor groove. These findings may explain specificity of suppression by ethoxidine of the strong top I cleavage sites with the A(+1), T(-1) immediately adjacent to the strand cut. Fagaronine does not show any sequence specificity of DNA intercalation, but its highly electronegative oxygen of hydroxy group (absent in ethoxidine) is shown to be an acceptor of the hydrogen bond with the NH(2) group of G base of DNA. Ability of fagaronine to stabilize top I-mediated ternary complex is proposed to be determined by interaction of its hydroxy group with the guanine at position (+1) of the DNA cleavage site and of quaternary nitrogen interaction with top I. The model proposed provides a guidance for screening new top I-targeted drugs in terms of identification of molecular determinants responsible for their top I inhibition effects.     

A novel cytotoxic ternary copper(II) complex of 1,10-phenanthroline and L-threonine with DNA nuclease activity

A novel ternary copper(II) complex, [Cu(phen)(L-Thr)(H2O)](ClO4) (phen=1,10-phenanthroline, L-Thr=L-threonine), has been synthesized and structurally characterized. The complex crystallized in a triclinic system with space group P1 , a=7.526(15) A, b=11.651(2) A, c=12.127(2) A, alpha=115.41(3) degrees , beta=102.34(3) degrees and gamma=91.33(3) degrees . The copper(II) center is situated in a distorted square-pyramidal geometry. At a concentration of 10(-6) mol L(-1), the complex exhibited potent cytotoxic effects against human leukemia cell line HL-60 and human stomach cancer cell line SGC-7901 with inhibition rates of over 90%, however, less pronounced effects were observed for human liver carcinoma cell line BEL-7402 and human non-small-cell lung cancer cell line A-549. The complex was shown to bind DNA by intercalation and cleave pBR322 DNA in the presence of ascorbate.     

Synthesis, crystal structure and action on Escherichia coli by microcalorimetry of copper complexes with 1,10-phenanthroline and amino acid

Copper complexes: [Cu(phen)(L-Ser)(H₂O)Cl] (1), [Cu(phen)(Gly)(H₂O)]Cl·3H₂O (2), [Cu(phen)(L-Ala)(H₂O)]Cl·H₂O (3), [Cu(phen)(L-Phe)(H₂O)]Cl·2.5H₂O (4), Cu(phen)₂Cl₂·6H₂O (5) (phen = 1,10-phenanthroline) were synthesized and characterized. The structure of 1 was characterized by X-ray crystallography and showed in a triclinic system with space group P1, a = 6.8953(15) Å, b = 10.737(2) Å, c = 11.894(3) Å, α = 110.395(3)°, β = 94.183(4)° and γ = 100.540(3)°. The antibacterial activities on Escherichia coli (E. coli) of these five copper complexes and CuCl₂ (6) were investigated by microcalorimetry. By analyzing the obtained metabolic thermogenic data and curves, crucial parameters such as rate constant of bacterial growth (k), half inhibitory concentration (IC₅₀), and generation time (t_G) were determined. All these copper complexes could stimulate the growth of the E. coli at their lower concentration. At their higher concentration they all showed antibacterial action. The inhibition on E. coli was 5 > 1 ≈ 2 ≈ 3 ≈ 4 > 6. And the antibacterial mechanism was discussed preliminarily.