DNA hydrolysis by rare-earth metal ions.

Plasmid DNA and poly(dA) are cleaved by rare-earth(III) ions at pH 7-8 and 50 degrees C. The cleavage has been confirmed by prompt conversion of supercoiled pBR 322 plasmid DNA (Form I) to a relaxed Form II. Furthermore, degradation of poly(dA) to shorter oligonucleotides is clearly evidenced by HPLC. A possible application of the metal ions (and their complexes) to artificial nucleases is indicated.     

Inhibition of cellulase-catalyzed lignocellulosic hydrolysis by iron and oxidative metal ions and complexes

Enzymatic lignocellulose hydrolysis plays a key role in microbially driven carbon cycling and energy conversion and holds promise for bio-based energy and chemical industries. Cellulases (key lignocellulose-active enzymes) are prone to interference from various noncellulosic substances (e.g., metal ions). During natural cellulolysis, these substances may arise from other microbial activities or abiotic events, and during industrial cellulolysis, they may be derived from biomass feedstocks or upstream treatments. Knowledge about cellulolysis-inhibiting reactions is of importance for the microbiology of natural biomass degradation and the development of biomass conversion technology. Different metal ions, including those native to microbial activity or employed for biomass pretreatments, are often tested for enzymatic cellulolysis. Only a few metal ions act as inhibitors of cellulases, which include ferrous and ferric ions as well as cupric ion. In this study, we showed inhibition by ferrous/ferric ions as part of a more general effect from oxidative (or redox-active) metal ions and their complexes. The correlation between inhibition and oxidation potential indicated the oxidative nature of the inhibition, and the dependence on air established the catalytic role that iron ions played in mediating the dioxygen inhibition of cellulolysis. Individual cellulases showed different susceptibilities to inhibition. It is likely that the inhibition exerted its effect more on cellulose than on cellulase. Strong iron ion chelators and polyethylene glycols could mitigate the inhibition. Potential microbiological and industrial implications of the observed effect of redox-active metal ions on enzymatic cellulolysis, as well as the prevention and mitigation of this effect in industrial biomass conversion, are discussed.     

Double-strand DNA hydrolysis by dilanthanide complexes

 Although there has been progress in developing artificial hydrolytic DNA cleaving agents, none of these has been shown to carry out the double-strand hydrolysis of DNA. We demonstrate that La(III) or Ce(IV) combined with the ligand 1,3-diamino-2-hydroxypropane-N,N,N′,N′-tetraacetate (HPTA) in a 2 : 1 ratio can efficiently cleave supercoiled plasmid DNA at 55  °C within a 3-h period. Analysis of end-labeled restriction fragments cleaved by these complexes reveals 3′- and 5′-ends consistent with a hydrolytic mechanism. Unlike for other polydentate carboxylate complexes, plasmid DNA cleavage by La₂(HPTA) or Ce₂(HPTA) affords a significant amount of linear DNA with a considerable fraction of the supercoiled form still remaining. This result implies that La₂(HPTA) and Ce₂(HPTA) can carry out double-strand cleavage of plasmid DNA. La₂(HPTA) and Ce₂(HPTA) represent the first metal complexes demonstrated to be capable of double-strand hydrolytic cleavage of plasmid DNA. Received: 29 March 1999 / Accepted: 9 July 1999     

Multifunctional catalysis by metal complexes: 1. Ester hydrolysis catalyzed by oximinatozinc(II) ions

Hydrolysis of p-nitrophenyl acetate catalyzed by a Zn(II) complex of 2-acetylpyridineketoxime or 2-pyridinecarboxaldoxime was studied as a model of multifunctional catalysis by metalloproteases. The reaction proceeded exclusively through the formation of an acylcatalyst intermediate under the experimental conditions, and both the formation and the breakdown of the acyl intermediate were much faster than the spontaneous reaction. The metal ion, the metal-bound water molecule or hydroxide ion, the oximate ion, and general bases contributed to the multifunctional catalysis in ester hydrolysis by the oximinatozinc(II) ions.     

Inhibition of vitamin K-dependent carboxylase by metal ions and metal complexes: a reassessment

The vitamin K-dependent enzymatic carboxylation of glutamyl residues in blood protein precursors and in synthetic peptides is inhibited in vitro by transition metal complexes. Some authors suggested it is a result of metal ions interaction with intermediary oxygenated species. Using an oxygraph we have observed increases in the rate of oxygen utilization in the carboxylating system containing reduced vitamin K after addition of some transition metal ions and complexes. Kinetic studies indicate that, although oxygen utilization is increased by the addition of Cu2+, Fe3+, and hematin, the initial rate of carboxylation is not affected. The rate of carboxylation rapidly decreases at oxygen concentrations below 50 microM and reaches zero when oxygen is depleted. UV spectroscopy revealed simultaneous acceleration of the conversion of vitamin K hydroquinone into the parent quinone. The magnitude of these effects, as well as carboxylation inhibition, depends on the oxidation potential of the complexed ion and its lipophilicity. Addition of stable Mn parallel ion, which has no inhibitory effect on carboxylation, does not increase the rate of oxygen utilization nor the hydroquinone oxidation. The results suggest that inhibition of carboxylation by transition metals is mainly due to depletion of the necessary components (oxygen, vitamin K hydroquinone) of the carboxylating system rather than quenching of activated, oxygen-containing intermediates.     

Enhanced hydrolysis of a phosphonate ester by mono-aquo metal cation complexes

The hydrolysis of the ester 2,4-dinitrophenyl- ethyl methylphosphonate has been examined by both stop-flow spectrophotometric and pH-stat techniques. These reactions have been carried out in the presence of several nucleophiles including simple non-labile (w.r.t. substitution) mono-aquo metal ion complexes. Comparison of reaction rates of the metal complexes with sterically hindered organic nucleophiles has led to the conclusion that the metal ions function predominantly as general base catalysts in dilute aqueous solution. Reaction rates for the various nucleophiles studied are tabulated together with solvolysis constants for hydroxide ion and water at 35 °C and I=0.1 mol dm⁻³ (KNO₃). These later two values are respectively 32.7 mol⁻¹ dm³ s⁻¹ and 1.37 x 10⁻⁴ s⁻¹. A Brönsted β value of 0.52 for the phosphonate ester studied has also been derived.     

Phosphate diester hydrolysis in biological relevant compounds by dinuclear metal complexes

The dinuclear Ni²⁺ and Zn²⁺ complexes of 1,1^′-[(1H-pyrazole-3,5-diyl)bismethylene]-bis(octahydro-1H-1,4,7-triazonine) induce phosphate diester hydrolysis in biological relevant substrates such as thymidine 5^′-monophosphate 4-nitrophenylester (TMPNP), guanosine (2^′-3^′) cyclic phosphate ((2^′-3^′)cGMP), guanylyl (2^′-5^′) guanosine ((2^′-5^′)GpG), adenylyl (3^′-5^′) adenosine ((3^′-5^′)ApA), and (2^′-deoxy)adenylyl (3^′-5^′) (2^′-deoxy)adenosine ((3^′-5^′)dApdA). Quantitative measurements of the hydrolysis of TMPNP indicate a Michaelis-Menten mechanism in which the substrate is bound by the dinuclear complex and is hydrolyzed by an intramolecular attack of a coordinated OH⁻ group. Qualitative HPLC measurements of the hydrolysis of the dinucleotide show that in the case of (2^′-5^′)GpG a cyclic phosphate is formed which then hydrolyses to 2^′-GMP and 3^′-GMP. The hydrolysis of (2^′-3^′)cGMP also gave, induced by the dinuclear Zn²⁺ complex, 2^′-GMP and 3^′-GMP.     

Superoxide and hydrogen peroxide suppression by metal ions and their EDTA complexes

Redox-active metal ions such as Fe(II)\(III) and Cu(I)\(II) have been proposed to activate reactive oxygen and nitrogen species (RONS) and thus, perpetuate oxidative damage. Here, we show that concentrations of metal ions and EDTA complexes with superoxide-destroying activities equivalent to 1 U SOD are Fe(III) 5.1 microM, Mn(II) 0.77 microM, Cu(II)-EDTA 3.55 microM, Fe(III)-EDTA 2.34 microM, and Mn(II)-EDTA 1.38 microM. The most active being the aquated Cu(II) species which exhibited superoxide-destroying activity equivalent to 2U of SOD at 0.29 microM. Hydrogen peroxide-destroying activities were as follows Fe(III)-EDTA ca. 70 U/mg and aquated Fe(III) 141 U/mg. In contrast, DTPA prevented superoxide-destroying activity and significantly depleted hydrogen peroxide-destroying activity. In conclusion, non-protein bound transition metal ions may have significant anti-oxidant effects in biological systems. Caution should be employed in bioassays when chelating metal ions. Our results demonstrate that DTPA is preferential to EDTA for inactivating redox-active metal ions in bioassays.     

Multiple metal ions drive DNA association by PvuII endonuclease

Restriction enzymes serve as important model systems for understanding the role of metal ions in phosphodiester hydrolysis. To this end, a number of laboratories have reported dramatic differences between the metal ion-dependent and metal ion-independent DNA binding behaviors of these systems. In an effort to illuminate the underlying mechanistic details which give rise to these differences, we have quantitatively dissected these equilibrium behaviors into component association and dissociation rates for the representative PvuII endonuclease and use these data to assess the stoichiometry of metal ion involvement in the binding process. The dependence of PvuII cognate DNA on Ca(II) concentration binding appears to be cooperative, exhibiting half-saturation at 0.6 mM metal ion and yielding an n(H) of 3.5 +/- 0.2 per enzyme homodimer. Using both nitrocellulose filter binding and fluorescence assays, we observe that the cognate DNA dissociation rate (k(-)(1) or k(off)) is very slow (10(-)(3) s(-)(1)) and exhibits a shallow dependence on metal ion concentration. DNA trap cleavage experiments with Mg(II) confirm the general irreversibility of DNA binding relative to cleavage, even at low metal ion concentrations. More dramatically, the association rate (k(1) or k(on)) also appears to be cooperative, increasing more than 100-fold between 0.2 and 10 mM Ca(II), with an optimum value of 2.7 x 10(7) M(-)(1) s (-)(1). Hill analysis of the metal ion dependence of k(on) indicates an n(H) of 3.6 +/- 0.2 per enzyme dimer. This value is consistent with the involvement in DNA association of two metal ions per subunit active site, a result which lends new strength to arguments for two-metal ion mechanisms in restriction enzymes.     

Winding of the DNA helix by divalent metal ions.

When supercoiled pBR322 DNA was relaxed at 0 or 22 degrees C by topoisomerase I in the presence of the divalent cations Ca2+, Mn2+ or Co2+, the resulting distributions of topoisomers observed at 22 degrees C had positive supercoils, up to an average delta Lk value of +8.6 (for Ca2+at 0 degrees C), corresponding to an overwinding of the helix by 0.7 degrees/bp. An increase of the divalent cation concentration in the reaction mixture above 50 mM completely reversed the effect. When such ions were present in agarose electrophoresis gels, they caused a relaxation of positively supercoiled DNA molecules, and thus allowed a separation of strongly positively supercoiled topoisomers. The effect of divalent cations on DNA adds a useful tool for the study of DNA topoisomers, for the generation as well as separation of positively supercoiled DNA molecules.     

Interaction of mithramycin with metal ions and DNA

The interaction of mithramycin with metal ions has been studied by absorbance and fluorescence spectroscopy. Magnesium shifts the drug absorbance spectrum to longer wavelengths and displays a weak binding constant (Kd = 1mM); no interaction with calcium was detected. The drug requires magnesium for binding to DNA and this is characterised by small additional hypochromic and bathochromic changes. Mithramycin does not bind to DNA in the presence of calcium. With 10mM magnesium the drug binds to DNA with an association constant of 9.2 x 10(4) M-1. The inability of calcium to substitute for magnesium has been confirmed by 'footprinting' experiments using both DNase I and hydroxyl radicals.     

Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.

The rate constant for the phosphoryl transfer step in site-specific DNA cleavage by EcoRV endonuclease has been determined as a function of pH and identity of the required divalent metal ion cofactor, for both wild-type and T93A mutant enzymes. These measurements show bell-shaped pH-rate curves for each enzyme in the presence of Mg2+ as a cofactor, indicating general base catalysis for the nucleophilic attack of hydroxide ion on the scissile phosphate, and general acid catalysis for protonation of the leaving 3'-O anion. The kinetic data support a model for phosphoryl transfer based on wild-type and T93A cocrystal structures, in which the ionizations of two distinct metal-ligated waters respectively generate the attacking hydroxide ion and the proton for donation to the leaving group. The model concurs with recent observations of two metal ions bound in the active sites of the type II restriction endonucleases BamHI and BglI, suggesting the possibility of a similar catalytic mechanism functioning in many or all members of this enzyme family.     

Interaction of DNA with divalent metal ions

The interaction between the native DNA macromolecules and Ca2+, Mn2+, Cu2+ ions in solutions of low ionic strength (10(-3) M Na+) is studied using the methods of differential UV spectroscopy and CD spectroscopy. It is shown that the transition metal ions Mn2+ exercise binding to the nitrogen bases of DNA at concentrations approximately 5 x 10(-6) M and form chelates with guanine of N7-Me(2+)-O6 type. Only at high concentrations in solution (5 x 10(-3) M) do Ca2+ ions interact with the nitrogen bases of native DNA. In the process of binding to Ca2+ and Mn2+ the DNA conformation experiences some changes under which the secondary structure of the biopolymer is within the B-form family. The DNA transition to the new conformation is revealed by its binding to Cu2+ ions.     

Comutagenicity and inhibition of DNA repair by metal ions in mammalian cells

Mutagenic and/or carcinogenic metal compounds may act directly by interaction with DNA and/or indirectly by interference with genetic control and repair mechanisms. In a previous report, we investigated the mutagenicity and comutagenicity of nickel (II) in the V79 Chinese hamster HGPRT-assay. Our present findings demonstrate that like nickel(II), chromium(VI) and cadmium(II) are also comutagenic with UV. Furthermore, there is only a weak concordance with comutagenic effects observed in bacterial test systems. In the case of nickel(II), there is a good correlation between comutagenicity and inhibition of DNA repair, as determined by using the nucleoid sedimentation technique with HeLa cells. This inhibition may occur via replacement of other divalent ions essential in repair enzymes.     

Alpha-glucosidase inhibitory effect of anti-diabetic metal ions and their complexes

We found alpha-glucosidase inhibitory (α-GI) effect of metal ions and their complexes which showed the high blood glucose lowering effect in diabetic model animals. The Cu(II) ion and its complexes showed strong α-GI activity greater than clinically used acarbose in in vitro studies. Furthermore, in in vivo experiments, α-GI action was newly discovered in normal ddy mice. These results suggested that one of action mechanisms of the anti-diabetic metal ions and complexes is related to the α-GI effects.     

Phosphodiester hydrolysis and specific DNA binding and cleavage promoted by guanidinium-functionalized zinc complexes

Two new Zn(II) complexes containing guanidinium groups, [Zn(L¹)Cl₂](ClO₄)₂ · H₂O · CH₃OH (1) and [Zn(L²)Cl₂](ClO₄)₂ · 0.5H₂O (2), were synthesized and characterized (L¹ = 5,5′-di[1-(guanidyl)methyl]-2,2′-bipyridyl bication and L² = 6,6′-di[1-(guanidyl)methyl]-2,2′-bipyridyl bication). Both complexes are able to catalyze bis(p-nitrophenyl) phosphate (BNPP) hydrolysis efficiently. Obtained kinetic data reveal that both 1 and 2 show nearly 300- and 600-fold rate enhancement of BNPP hydrolysis, respectively, compared to their simple analogue without the guanidinium groups [Zn(bpy)Cl₂] (bpy = 2,2′-bipyridy) (3). Enhanced acceleration for cleavage of BNPP could be attributed to cooperative interaction between the Zn(II) ion and the guanidinium groups by electrostatic interaction and H-bonding. Studies on inhibition of sequence-specific endonucleases (DraI and SmaI) by complexes show that 1 and 2 are able to recognize nucleotide sequence, -TTT^AAA-, and highly effectively cleave the plasmid DNA in the presence of hydrogen peroxide, while 3 has no specific binding to the DNA target sequences and only shows low DNA cleavage activity.     

Rare earth metal ions for unprecedentedly fast RNA hydrolysis.

Adenylyl(3'-5')adenosine (ApA) and uridyl(3'-5')uridine (UpU) are hydrolyzed at unprecedentedly large rates by rare earth metal ions at pH 8, 30 degrees C. With 0.01 M Tm(III), the half-lives are 10 min and 51 min, respectively. Potentiality of these ions as catalytic center of artificial ribonuclease is proposed.     

Cleavage of parallel-stranded DNA duplex by peplomycin metal complexes.

Peplomycin-mediated degradation of parallel-stranded (ps) duplex was investigated. It was found that Co- and Fe-peplomycins degraded ps DNA duplex by 4'-hydrogen abstraction at 5'-GPy (pyrimidine) site in a similar manner to that of antiparallel B-DNA. While the orientation of two strands of ps and B-form DNA duplexes are reversed, peplomycin metal complex can bind to ps DNA duplex to cause oxidative DNA damage. These results indicate that peplomycin metal complex mainly interacts with one strand which is damaged.     

Coordinated cations in dipicolinato complexes of divalent metal ions

Several salts of alkali, alkaline earth metal and organic ammonium cations of a complex anion [ML₂]²⁻ {Where L = dipicolinato dianion, M = copper(II), nickel(II) and zinc(II)} are prepared. The coordination effect of [ML₂]²⁻ with the cations such as sodium, potassium, calcium, magnesium, and organic cations namely diammonium cation of 1,5-pentanediamine, diammonium cation of 1,8-octyldiamine, mono ammonium cation of 4-aminobenzylamine are studied by determining their X-ray crystal structures. Depending on the nature of cations, four different types of structures are obtained. When calcium is the cation a polymeric structure with calcium ions bridging the [ML₂]²⁻ is observed. The salts having sodium and potassium cations form polymeric chain like structures by oxo and aqua bridges. In the case of magnesium, the hydrated form of magnesium cations coordinates to [ML₂]²⁻. The organic ammonium salts of [ML₂]²⁻ have the structural features of conventional ionic complexes. These salts easily exchange cations. The organic ammonium salts of [ML₂]²⁻ decomposes to give the corresponding metal oxides at relatively low temperature range 300-450 °C.     

Antioxidant properties of complexes of flavonoids with metal ions

The formation of complexes of metal ions with the flavonoids quercetin (L1), rutin (L2), galangin (L3) and catechin (L4) has been investigated by UV-visible spectroscopy. The antioxidant activities of the compounds were evaluated by using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicalscavenging method. In this work, we have shown that the complexed flavonoids are much more effective free radical scavengers than the free flavonoids. We suggest that the higher antioxidant activity of the complexes is due to the acquisition of additional superoxide dismutating centers. Radical scavenging activities of the compounds were also investigated from an electrochemical point of view. There is a relationship between the logarithm of the antioxidant activity (represented by EC50) and the oxidation potential. The synergic effect of the complexes and ascorbic acid were studied by [13C]-NMR analyses. The results show that ascorbic acid can protect flavonoids from oxidative degradation, and reveal antioxidant synergies between ascorbic acid and the compounds.