Double-strand hydrolysis of plasmid DNA by dicerium complexes at 37 degrees C

Crystal structure of Ce(IV)/dipicolinate complex as catalyst for DNA hydrolysis

The structures of Ce(4+) complexes that are active for DNA hydrolysis were determined for the first time by X-ray crystallography. The crystals were prepared from a 1:2 mixture of Ce(NH(4))(2)(NO(3))(6) and dipicolinic acid (2,6-pyridinedicarboxylic acid). Depending on the recrystallization conditions, three types of crystals were obtained. Some of the Ce(4+) ions in these complexes have enough coordinated water molecules that can directly and indirectly participate in the catalysis. The distances between the Ce(4+) and the dipicolinate ligand are considerably shorter than those in the corresponding La(3+) and Ce(3+) complexes. On the other hand, the distances between the Ce(4+) and its coordinated water are similar to those for the La(3+) and Ce(3+) complexes. In a proposed mechanism of DNA hydrolysis, the scissile phosphodiester linkage is notably activated by coordination to Ce(4+) and attacked by the Ce(4+)-bound hydroxide. The process is further assisted by acid catalysis of Ce(4+)-bound water.

Synthesis and DNA-Cleavage Properties of Metal Complexes of 1,4,7,10-Tetraazacyclododecane (Cyclen) Functionalized with a Pendant Benzocrown Ether

The synthesis and DNA-cleavage properties of a series of novel mononuclear Zn(II), Cu(II), and Co(II) complexes 2 of a crown-ether-functionalized cyclen ligand is described. The Cu complex 2b displayed the highest catalytic activity towards pUC 19 DNA. The effects of reaction time, complex concentration, and pH were investigated, showing that 2b readily and efficiently converts supercoiled (type I ) plasmid DNA to nicked (type II) DNA under physiological conditions (37 degrees, pH 7.4).

Formation and Stability of Mononuclear and Dinuclear Eu(III) Complexes and Their Catalytic Reactivity Toward Cleavage of an RNA Analog

The complex between Eu(III) and 1,7-diaza-4,10,13-trioxacyclopentadecane-N,N'-diacetic acid (L4) was characterized by pH potentiometric titration and 1H NMR spectroscopy. The conversion of the monomer to a dimeric complex is observed as the pH is increased from 7 to 10 in a reaction that releases one mol/HO- per dimer formed. The dimeric complex undergoes a further ionization with a pKa of 10.7. Kinetic parameters are reported for the cleavage of the simple phosphodiester 2-hydroxypropyl-4-nitrophenyl phosphate catalyzed by both the monomeric and the dimeric Eu(III) complexes. These data show that the monomer and dimer stabilize their bound reaction transition states with similar free energies of 7.1 and 7.6 kcal/mol, respectively. Clearly, a bridging hydroxide is not an optimal linker to promote cooperative catalysis between Eu(III) centers in macrocycles with multiple polyaminocarboxylate pendent groups.

Synthesis and DNA Binding/Cleavage of Mononuclear Copper(II) Phenanthroline/Bipyridine Proline Complexes

The complexes [Cu(II)(phen)(L-Pro)(H2O)]+ ClO4(-) (1; phen = 1,10-phenanthroline) and [Cu(II)(bipy)(L-Pro)(H2O)]+ ClO4(-) (2; bipy = 2,2'-bipyridine) were synthesized and characterized by IR, magnetic susceptibility, UV/VIS, EPR, ESI-MS, elemental analysis, and theoretical calculations. The metal center was found in a square-pyramidal geometry. UV/VIS, thermal-denaturation, and fluorescence-spectroscopic studies were conducted to assess the interaction of the complexes with CT-DNA. An intercalative mode of binding was found, with intrinsic binding constants (Kb) of 3.86x10(3) and 4.6x10(3) M(-1) and Stern-Volmer quenching constants (K) of 0.15 and 0.11 for 1 and 2, respectively. Interestingly, none of the Cu(II) complexes was able to cleave pUC-19 DNA, which is attributed to the absence of a Pro amide H-atom and inhibition of the formation of an OH radical from the axially coordinated H2O molecule.

Hydrolytic cleavage of DNA by quercetin manganese(II) complexes

Quercetin manganese(II) complexes were investigated focusing on its DNA hydrolytic activity. The complexes successfully promote the cleavage of plasmid DNA, producing single and double DNA strand breaks. The amount of conversion of supercoiled form (SC) of plasmid DNA to the nicked circular form (NC) depends on the concentration of the complex as well as the duration of incubation of the complexes with DNA. The maximum rate of conversion of the supercoiled form to the nicked circular form at pH 7.2 in the presence of 100 microM of the complexes is found to be 1.32 x 10(-4) s(-1). The hydrolytic cleavage of DNA by the complexes was supported by the evidence from free radical quenching, thiobarbituric acid-reactive substances (TBARS) assay and T4 ligase ligation.

Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA

A monophosphate group was attached to the terminus of pseudo-complementary peptide nucleic acid (pcPNA), and two of thus modified pcPNAs were combined with Ce(IV)/EDTA for site-selective hydrolysis of double-stranded DNA. The site-selective DNA scission was notably accelerated by this chemical modification of pcPNAs. These second-generation artificial restriction DNA cutters (ARCUTs) differentiated the target sequence so strictly that no scission occurred even when only one DNA base-pair was altered to another. By using two of the activated ARCUTs simultaneously, DNA substrate was selectively cut at two predetermined sites, and the desired fragment was clipped and cloned. The DNA scission by ARCUT was also successful even when the target site was methylated by methyltransferase and protected from the corresponding restriction enzyme. Furthermore, potentiality of ARCUT for manipulation of huge DNA has been substantiated by site-selective scission of genomic DNA of Escherichia coli (composed of 4,600,000 bp) at the target site. All these results indicate promising applications of ARCUTs for versatile purposes.

Hydrolytic cleavage of DNA by quercetin zinc(II) complex

Quercetin zinc(II) complex was investigated focusing on its hydrolytic activity toward DNA. The complex successfully promotes the cleavage of plasmid DNA, producing single and double DNA strand breaks. The amount of conversion of supercoiled form (SC) of plasmid to the nicked circular form (NC) depends on the concentration of the complex as well as the duration of incubation of the complex with DNA. The rate of conversion of SC to NC is 1.68x10(-4) s(-1) at pH 7.2 in the presence of 100 microM of the complex. The hydrolytic cleavage of DNA by the complex is supported by the evidence from free radical quenching, thiobarbituric acid-reactive substances (TBARS) assay, and T4 ligase ligation.

Synthesis and DNA Cleavage Activity of Artificial Receptor 1,4,7-Triazacyclononane Containing Guanidinoethyl and Hydroxyethyl Side Arms

A novel phosphodiester receptor 1-(2-guanidinoethyl)-4-(2-hydroxyethyl)-1,4,7-triazacyclononane hydrochloride 1 was synthesized. DNA cleavage efficiency of 1 exhibits remarkable increases compared with its ZnII complex and corresponding nonguanidinium compound N-(2-hydroxyethyl)-1,4,7-triazacyclononane and parent 1,4,7-triazacyclononane. Kinetic data of DNA cleavage promoted by 1 fit to a Michaelis-Menten-type equation with kmax of 0.160 h-1 giving 107-fold rate acceleration over uncatalyzed DNA. The acceleration is driven by the spatial proximity of the nucleophilic hydroxyl group and the electrophilic activation for the phosphodiester by the guanidinium group.

The crystal structure, self-assembly, DNA-binding and cleavage studies of the [2]pseudorotaxane composed of cucurbit[6]uril

The [2]pseudorotaxanes of cucurbit[6]uril with guest molecule 1,6-bis(imidazol-1-yl)hexane (BIMH) were synthesized and characterized by ESI-MS spectrometry, (1)H NMR spectra, and X-ray diffraction crystallography. The influence of different anions on self-assembly in solid-state was discussed by X-ray diffraction crystallography. However, more interestingly, and to our amazement, we discovered the CB[6]/BIMH [2]pseudorotaxane exhibiting efficient cleavage of pBR322 DNA in physiological environment. The cleavage mechanism were studied by fluorescence spectra and the hydrolysis of bis(2,4-dinitrophenyl)-phosphate (BDNPP). From DNA-binding mode being electrostatic force and the first-order kinetics equation, we prove indirectly that the mechanism may be hydrolytic cleavage.

Effects of N-alkyl and ammonium groups on the hydrolytic cleavage of DNA with a Cu(II)TACH (1,3,5-triaminocyclohexane) complex. Speciation, kinetic, and DNA-binding studies for reaction mechanism

cis,cis-1,3,5-Triaminocyclohexane (c-TACH), its N-alkyl-derivatives (alkyl = methyl, ethyl), and trans,cis-1,3,5-triaminocyclohexane (t-TACH) were prepared, and speciation and DNA cleaving property of Cu(II) complexes of these ligands were investigated. All of the complexes efficiently promote the hydrolytic cleavage of supercoiled plasmid DNA under physiological conditions without further additives. The DNA cleavage rate (V(obs)) trend at pH values between 8 and 9 is N-Me(3) = N-Et(1) < t-TACH < c-TACH < N-Et(2) < N-Et(3). At pH 7, the trend is c-TACH < N-Et(3) = N-Et(2) < N-Et(1) < N-Me(3) << t-TACH. The cleavage rate constants at 35 degrees C, for the c-TACH complex are 3 x 10(-1) h(-1) at pH 8.1 and 2 x 10(-1) h(-1) at pH 7.0 ([DNA] = 7 microM, [Cu(II)-complex] = 105 microM). The hydrolytically active species at pH > 8 is CuL(H(2)O)(OH)(+) in which L coordinates to Cu(II) as a tridentate ligand for all complexes except for t-TACH. The hydrolytically active species at pH 7 is CuLH(H(2)O)(3)(3+) or CuLH(H(2)O)(4)(3+) in which LH coordinates as bidentate ligand. DNA-binding constants of c-TACH and t-TACH complexes are presented and the effects of N-alkyl and ammonium groups are discussed in light of the proposed reaction mechanism.

Metal-binding and nuclease activity of an antimicrobial peptide analogue of the salivary histatin 5

The salivary antimicrobial peptide histatin 5 is characterized by its cationic nature, structural flexibility, and the presence of two metal-binding sites (the ATCUN motif and a Zn-binding motif). These properties make this peptide a good model for the design of new drugs of low molecular weight. In this work, we have synthesized and studied a new peptide, an analogue of the histatin 5 named ATCUN-C16, which contains both metal-binding centers. The results show that our 20-residue-derived peptide preserves anticandidal activity and exhibits a higher propensity to assume a stable conformation in a hydrophobic environment than do histatin 5 and the C16 peptide that contains the 16 residues of the C-terminal part of histatin 5, although overall our peptide remains a flexible molecule. ACTUN-C16 was found to bind DNA in a gel retardation assay and to have a nuclease activity in the presence of copper and zinc ions and ascorbate. Its nuclease activity can be attributed to the synergistic action of oxidative and hydrolytic activities due to the Cu-ATCUN complex and to the zinc ion coordination, respectively. The results show a new property of this family of salivary peptides and suggest a novel use of this peptide as a small nuclease and biotechnological tool.

Active species for Ce(IV)-induced hydrolysis of phosphodiester linkage in cAMP and DNA

The hydrolysis of cyclic adenosine 3',5'-monophosphate and 2'-deoxythymidylyl(3'-5')2'-deoxythymidine by Ce(NH4)2(NO3)6 was kinetically studied. The rate of hydrolysis was fairly proportional to the concentration of [Ce2(IV) (OH)4]4+ , showing that this is the catalytically active species. According to quantum-chemical calculation, the two Ce(IV) ions in this [Ce2(IV) (OH)4]4+ cluster are bridged by two OH residues. Upon the complex formation with H2 PO4- (a model compound for the phosphodiesters), these two Ce(IV) ions bind the two oxygen atoms of the substrate and enhance the electrophilicity of the phosphorus atom. The catalytic mechanism of Ce(IV)-induced hydrolysis of phosphodiesters has been proposed on the basis these results.

Double strand DNA cleavage with a binuclear iron complex

Covalently linking two single strand DNA cleaving agents resulted in a new biomimetic binuclear iron complex capable of effecting oxidative double strand DNA cleavage.

Synthesis and DNA cleavage activities of mononuclear macrocyclic polyamine zinc(II), copper(II), cobalt(II) complexes which linked with uracil

Mononuclear macrocyclic polyamine zinc(II), copper(II), cobalt(II) complexes, which could attach to peptide nucleic acid (PNA), were synthesized as DNA cleavage agents. The structures of these new mononuclear complexes were identified by MS and (1)H NMR spectroscopy. The catalytic activities on DNA cleavage of these mononuclear complexes with different central metals were subsequently studied, which showed that copper complex was better catalyst in the DNA cleavage process than zinc and cobalt complexes. The effects of reaction time, concentration of complexes were also investigated. The results indicated that the copper(II) complexes could catalyze the cleavage of supercoiled DNA (pUC 19 plasmid DNA) (Form I) under physiological conditions to produce selectively nicked DNA (Form II, no Form III produced) with high yields. The mechanism of the cleavage process was also studied.

DNA hydrolysis promoted by 1,7-dimethyl-1,4,7,10-tetraazacyclododecane

Several acyclic and macrocyclic polyamines were evaluated for their ability to cleave DNA. 1,7-Dimethyl-1,4,7,10-tetraazacyclododecane (DMC) could hydrolyze double-strand DNA at a concentration of 25microM. pH 7.2 was the optimal condition to cleave DNA in the presence of DMC. Supercoiled DNA hydrolytic cleavage by DMC was supported by the evidence from free radical quenching and T4 ligase ligation.

Hydrolysis of plasmid DNA and RNA by amino alkyl naphthalimide as metal-free artificial nuclease

A strategy of dimethylamino alkyldiimide conjugated with an intercalator of naphthalimide for hydrolysis of DNA was suggested and evaluated. 4 can hydrolyze 4 kb plasmid DNA into 2 kb fragments with GC and GG selectivity, which represents a novel example of sequence- or site-selective metal-free DNA artificial nuclease. Results also show it could hydrolyze RNA efficiently.

Ternary Nickel(II) Complexes as Hydrolytic DNA-Cleavage Agents

A series of small model complexes made from Ni(II) and the ligands ethylenediamine (en), histamine (hist), and histidylleucine (HisLeu) were prepared and studied as potential hydrolytic DNA-cleavage agents. The stability constants and species-distribution curves for these complexes were determined as a function of pH. The 1 : 1 : 1 ternary complexes [Ni(II)(en)(HisLeu)] (1) and [Ni(II)(hist)(HisLeu)] (2) were the only major species present at the physiologically relevant pH of 6-7, as further corroborated by ESI-MS analysis. The complex geometries of 1 and 2 were analyzed by UV/VIS experiments and molecular dynamics (MD) simulations. Both ternary complexes were found to intercalate with DNA, as shown by UV/VIS, thermal-denaturation, and fluorescence-titration studies with ethidium bromide (EB). The intrinsic binding constants (K(b)) for the bound complexes 1DNA and 2DNA were determined as 150 and 290, resp. Gel-electrophoresis experiments revealed that 1 and 2 cleave supercoiled (type-I) to nicked-circular (type-II) DNA at physiological pH, with rate constants of 0.64 and 0.75 h(-1), resp. A tentative mechanism for this hydrolytic cleavage is proposed.

Synthesis and characterisation of bis-cyclen based dinuclear lanthanide complexes

The design and synthesis of several bis-macrocyclic cyclen (1,4,7,10-tetraazacyclododecane) ligands and their corresponding lanthanum or europium complexes is described; these dinuclear lanthanide systems were made by connecting two macrocyclic cyclen moieties through a rigid, covalent, p-xylylenediamide bridge or a flexible aliphatic hexane bridge. These ligands were subsequently functionalised with six acetamide pendant arms (CONR1R2: R1 = R2 = H or CH3, or R1 = H, R2 = CH3). The corresponding lanthanide bis-complexes were then formed by reaction with La(III) and Eu(III) triflates, yielding overall cationic (+VI charged) complexes.

Kinetic and equilibrium studies on the polyazamacrocycle neotetren: metal-complex formation and DNA interaction

The macrocyclic polyamine 2,5,8,11,14-pentaaza[15]-[15](2,9)[1,10]phenanthrolinophane (neotetren) is studied in its ability to coordinate Cu(ii) even at very low pH values and to interact, as a metal complex, with DNA. The kinetics and equilibria for 1 : 1 and 2 : 1 metal-ligand complexes formation are studied by the stopped-flow method and UV spectrophotometry. Differently protonated complexes are formed, with rate constants much lower than that of water exchange at copper(II) and other Cu(II)/amine systems, this behaviour being ascribed to ring effects and intra-molecular hydrogen bonds. Concerning the DNA/copper(II)-neotetren complexes interaction, analysis of data suggests an intercalative mode of binding. The kinetic results for both DNA/CuL and DNA/Cu(2)L systems agree with the sequence D + S <-->D,S <-->DS where the metal complexes (D) react with the DNA sites (S) leading to fast formation of an externally bound form (D,S) which is converted into an intercalated complex (DS). A very slow process is also detected and ascribed to a conformational change in the polynucleotide secondary structure where the metal centre plays a crucial role. Chromatographic experiments demonstrate that both the investigated Cu(II)/L complexes are able to cleave DNA, but only in the presence of hydrogen peroxide.

Site-selective DNA hydrolysis by Ce(IV)-EDTA with the use of one oligonucleotide additive bearing two monophosphates

Two deoxyuridine derivatives each bearing a monophosphate group at the 5-position with a C3 linker, were incorporated into an oligonucleotide. By using this modified oligonucleotide, a bulge was formed at a predetermined position in a DNA substrate, and two monophosphate groups were placed at both junctions of the bulge. Upon treatment of the mixture with Ce(IV)-EDTA at pH 7.0, the phosphodiester linkages at the bulge site were selectively and efficiently hydrolyzed. The monophosphate groups introduced into the bulge site greatly accelerated site-selective DNA scission. Compared with the previously reported two-additive system, which combines two oligonucleotide additives each with a monophosphate at their termini, the present one-additive system is simpler and more convenient. Furthermore, site-selective DNA hydrolysis by using this one-additive system is successful even at high reaction temperatures (e.g., 55 degrees C). This reflects the thermodynamic stability of the duplexes formed between the substrate and the additive DNA.

Novel Peptide-Based Copper(II) Complexes for Total Hydrolytic Cleavage of DNA

Stable Cu(II) complexes with histamine- and histidine-containing dipeptides histidylserine and histidylphenylalanine have been developed. Their interaction in solution has been investigated, and the stability of their complexes was determined. The nature of binding in these complexes has been explained with the help of potentiometric pH titrations and 1H-NMR spectroscopy. The geometry of these complexes has been established by electronic spectra. The DNA-binding and -cleavage abilities of these Cu(II) complexes have been probed by the absorption, thermal denaturation, fluorescence, and electrophoresis experiments. The results suggest that these peptide-based Cu(II) complexes effectively bind and efficiently cleave DNA under mild biological conditions. Since Cu(II) complexes are known to play an important role in phosphodiester bond cleavages, these results assume importance.

Lanthanide-mediated phosphoester hydrolysis and phosphate elimination from phosphopeptides

Lanthanide ions can mediate both phosphomonoester hydrolysis and beta-elimination of inorganic phosphate from polypeptide substrates under near-physiological conditions of pH, temperature, and salt.

Macrocyclic Lanthanide Complexes as Artificial Nucleases and Ribonucleases: Effects of pH, Metal Ionic Radii, Number of Coordinated Water Molecules, Charge, and Concentrations of the Metal Complexes

We have been interested in the design, synthesis, and characterization of artificial nucleases and ribonucleases by employing macrocyclic lanthanide complexes because their high thermodynamic stability, low kinetic lability, high coordination number, and charge density (Lewis acidity) allow more design flexibility and stability. In this paper, we report the study of the use of the europium(III) complex, EuDO2A+ (DO2A is 1,7-dicarboxymethyl-1,4,7,10-tetraazacyclododecane) and other lanthanide complexes (i.e., LaDO2A+, YbDO2A+, EuK21DA+, EuEDDA+, and EuHEDTA where K21DA is 1,7-diaza-4,10,13-trioxacyclopentadecane-N,N'-diacetic acid, EDDA is ethylenediamine-N,N'-diacetic acid, and HEDTA is N-hydroxyethyl-ethylenediamine-N,N',N'-triacetic acid), as potential catalysts for the hydrolysis of the phosphodiester bond of BNPP (sodium bis(4-nitrophenyl)-phosphate). For the pH range 7.0-11.0 studied, EuDO2A+ promotes BNPP hydrolysis with the quickest rates among LaDO2A+, EuDO2A+, and YbDO2A+. This indicates that charge density is not the only factor affecting the reaction rates. Among the four complexes, EuDO2A+, EuK21DA+, EuEDDA+, and EuHEDTA, with their respective number of inner-sphere coordinated water molecules three, two, five, and three, EuEDDA+, with the greatest number of inner-sphere coordinated water molecules and a positive charge, promotes BNPP hydrolysis more efficiently at pH below 8.4, and the observed rate trend is EuEDDA+ > EuDO2A+ > EuK21DA+ > EuHEDTA. At pH > 8.4, the EuEDDA+ solution becomes misty and precipitates form. At pH 11.0, the hydrolysis rate of BNPP in the presence of EuDO2A+ is 100 times faster than that of EuHEDTA, presumably because the positively charged EuDO2A+ is more favorable for binding with the negatively charged phosphodiester compounds. The logarithmic hydrolysis constants (pKh) were determined, and are reported in the parentheses, by fitting the kinetic k(obs) data vs pH for EuDO2A+ (8.4), LaDO2A+ (8.4), YbDO2A+ (9.4), EuK21DA+ (7.8), EuEDDA+ (9.0), and EuHEDTA (10.1). The preliminary rate constant-[EuDO2A+] data at pH 9.35 were fitted to a monomer-dimer reaction model, and the dimer rate constant is 400 times greater than that of the monomer. The fact that YbDO2A+ catalyzes BNPP less effectively than EuDO2A+ is tentatively explained by the formation of an inactive dimer, [Yb(DO2A)(OH)]2, with no coordination unsaturation for BNPP substrate binding.

Oligonucleotide bearing ethylenediamine-N,N,N'-Triacetates for gap-selective DNA hydrolysis by Ce4+/EDTA

With the use of two oligonucleotides bearing ethylenediamine-N,N,N'-triacetate groups as additives, gap sites were formed at predetermined sites in substrate DNA. Upon treating these systems with a Ce(4+)/EDTA complex at pH 7.0 and 37 degrees C, the phosphodiester linkages at the gap site were selectively hydrolyzed. The DNA scission was greatly promoted by the introduction of ethylenediaminetriacetate groups, and the scission efficiency increased as the number of these groups increased. Even a one-base gap was successfully hydrolyzed when three ethylenediaminetriacetate groups were placed consecutively at both edges of the gap, although the scission was minimal in the absence of these groups. The site-selective scission could be also achieved at higher temperatures without any significant loss of site-selectivity.

DNA Cleavage by Copper−ATCUN Complexes. Factors Influencing Cleavage Mechanism and Linearization of dsDNA

The reactivity of two [peptide-Cu] complexes ([GGH-Cu](-) and [KGHK-Cu](+)) toward DNA cleavage has been quantitatively investigated. Neither complex promoted hydrolytic cleavage, but efficient oxidative cleavage was observed in the presence of a mild reducing agent (ascorbate) and dioxygen. Studies with scavengers of ROS confirmed hydrogen peroxide to be an obligatory diffusible intermediate. While oxidative cleavage of DNA was observed for Cu(2+)(aq) under the conditions used, the kinetics of cleavage and reaction products/pathway were distinct from those displayed by [peptide-Cu] complexes. DNA cleavage chemistry is mediated by the H(2)O-dependent pathway following C-4'H abstraction from the minor groove. Such a cleavage path also provides a ready explanation for the linearization reaction promoted by [KGHK-Cu](+). Kinetic activities and reaction pathways are compared to published results on other chemical nucleases. Both [peptide-Cu] complexes were found to display second-order kinetics, with rate constants k(2) approximately 39 and 93 M(-1) s(-1) for [GGH-Cu](-) and [KGHK-Cu](+), respectively. Neither complex displayed enzyme-like saturation behavior, consistent with the relatively low binding affinity and residence time expected for association with dsDNA, and the absence of a prereaction complex. However, the intrinsic activity of each is superior to other catalyst systems, as determined from relative k(2) or k(cat)/K(m) values. Linearization of DNA was observed for [KGHK-Cu](+) relative to [GGH-Cu](-), consistent with the increased positive charge and longer residency time on dsDNA.

An Asymmetric Dizinc Phosphodiesterase Model with Phenolate and Carboxylate Bridges

A phosphodiesterase model with two zinc centers has been synthesized and characterized. The compound, [Zn(2)(L(-)(2H))(AcO)(H(2)O)](PF(6)).2H(2)O (Zn(2)L'), was formed using an "end-off" type compartmental ligand, 2,6-bis{[(2-pyridylmethyl)(2-hydroxyethyl)amino]methyl}-4-methylphenol (L), and zinc acetate dihydrate. The X-ray crystallographic analysis shows that Zn(2)L' contains a mu-acetato-mu-cresolato-dizinc(II) core comprised of a quasi-trigonal bipyramidal Zn and a distorted octahedral Zn, and the distance between them is 3.421 Angstroms which is close to the dizinc distance in related natural metalloenzymes. Phosphodiesterase activity of Zn(2)L' was investigated using bis(4-nitrophenyl) phosphate (BNPP) as the substrate. The pH dependence of the BNPP cleavage in aqueous buffer media shows a sigmoid-shaped pH-k(obs) profile with an inflection point around pH 7.13 which is close to the first pK(a) value of 7.20 for Zn(2)L' obtained from the potentiometric titration. The catalytic rate constant (k(cat)) is 4.60 x 10(-6) s(-1) at pH 7.20 and 50 degrees C which is ca. 10(5)-fold higher than that of the uncatalyzed reaction. The deprotonated alcoholic group appended on Zn(2)L' is responsible for the cleavage reaction. The possible mechanism for the BNPP cleavage promoted by Zn(2)L' is proposed on the basis of kinetic and spectral analysis. The dizinc complex formed in situ in anhydrous DMSO exhibits a similar ability to cleave BNPP. This study provides a less common example for the phosphodiesterase model in which the metal-bound alkoxide is the nucleophile.

Efficient Plasmid DNA Cleavage by a Mononuclear Copper(II) Complex

The Cu(II) complex of the ligand all-cis-2,4,6-triamino-1,3,5-trihydroxycyclohexane (TACI) is a very efficient catalyst of the cleavage of plasmid DNA in the absence of any added cofactor. The maximum rate of degradation of the supercoiled plasmid DNA form, obtained at pH 8.1 and 37 degrees C, in the presence of 48 microM TACI.Cu(II), is 2.3 x 10(-3) s(-1), corresponding to a half-life time of only 5 min for the cleavage of form I (supercoiled) to form II (relaxed circular). The dependence of the rate of plasmid DNA cleavage from the TACI.Cu(II) complex concentration follows an unusual and very narrow bell-like profile, which suggests an high DNA affinity of the complexes but also a great tendency to form unreactive dimers. The reactivity of the TACI.Cu(II) complexes is not affected by the presence of several scavengers for reactive oxygen species or when measured under anaerobic conditions. Moreover, no degradation of the radical reporter Rhodamine B is observed in the presence of such complexes. These results are consistent with the operation of a prevailing hydrolytic pathway under the normal conditions used, although the failure to obtain enzymatic religation of the linearized DNA does not allow one to rule out the occurrence of a nonhydrolytic oxygen-independent cleavage. A concurrent oxidative mechanism becomes competitive upon addition of reductants or in the presence of high levels of molecular oxygen: under such conditions, in fact, a remarkable increase in the rate of DNA cleavage is observed.

Kinetics of phosphodiester cleavage by differently generated cerium(iv) hydroxo species in neutral solutions

Neutral aqueous solutions of cerium ammonium nitrate obtained by dilution of their acetonitrile stock solution with imidazole buffer show high catalytic activity in the hydrolysis of bis(p-nitrophenyl) phosphate (BNPP) and better reproducibility than other similar systems, but suffer from low stability. The kinetics of catalytic hydrolysis is second-order in Ce(IV), independent of pH in the range 5-8 and tentatively involves the Ce2(OH)7+ species as the active form. Attempts to stabilize the active species by different types of added ligands failed, but the use of Ce(IV) complexes pre-synthesized in an organic solvent with potentially stabilizing ligands as precursors of active hydroxo species appeared to be more successful. Three new Ce(IV) complexes, [Ce(Phen)2O(NO3)2], [Ce(tris)O(NO3)(OH)] and [Ce(BTP)2(NO3)4].2H2O (BTP = bis-tris propane, 1,3-bis[tris(hydroxymethyl)methylamino]propane), were prepared by reacting cerium ammonium nitrate with the respective ligands in acetonitrile and were characterized by analytical and spectroscopic techniques. Aqueous solutions of these complexes undergo rapid hydrolysis producing nearly neutral polynuclear Ce(IV) oxo/hydroxo species with high catalytic activity in BNPP hydrolysis. Potentiometric titrations of the solutions obtained from the complex with BTP revealed the formation of Ce4(OH)15+ species at pH > 7, which are protonated affording Ce4(OH)14(2+) and then Ce4(OH)13(3+) on a decrease in pH from 7 to 5. The catalytic activity increases strongly on going to species with a higher positive charge. The reaction mechanism involves first- and second-order in catalyst paths as well as intermediate complex formation with the substrate for higher charged species.

Artificial metallonucleases

The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is a fascinating challenge that will show the way to obtaining artificial nucleases able to compete with the natural enzymes. This Feature Article highlights the progress reported toward the realization of synthetic nucleases with particular attention to the strategies that can be pursued to improve efficiency and sequence selectivity.

Site-selective DNA hydrolysis by combining Ce(IV)/EDTA with monophosphate-bearing oligonucleotides and enzymatic ligation of the scission fragments

By using two oligonucleotide additives that bear a monophosphate group at the termini through various linkers, gap structures were formed at predetermined positions in substrate DNA, and the monophosphate groups were placed at both edges of these gaps. At pH 7.0 and 37 degrees C, the phosphodiester linkages in the gap sites were efficiently and selectively hydrolyzed by Ce(IV)/EDTA complex (EDTA = ethylenediamine-N,N,N',N'-tetraacetate). The linkages in the middle of the gaps were predominantly hydrolyzed. Compared with DNA scission using oligonucleotide additives that bear no terminal monophosphate, the present scission was much faster (22-fold for a 3-base gap and 14-fold for a 5-base gap) and more site selective. Introduction of one monophosphate group to either edge of the gaps was also effective for promotion of both site selectivity and scission rate. The monophosphate group(s) at the gap site recruits the Ce(IV) to the target site and magnifies the difference in intrinsic reactivity between the target site and the others. Even at higher reaction temperatures, the site selectivity remained satisfactorily high. Furthermore, the fragments formed by the site-selective scission were connected with various oligonucleotides by using DNA ligase, producing desired recombinant DNAs.

Intra and Intermolecular Magnetic Interactions in a Series of Dinuclear Cu(II)/hxta Complexes {H5hxta =N,N‘-(2-hydroxy-1,3-xylylene)-bis-(N-carboxymethylglycine)}: Correlation of Magnetic Properties with Geometry

Nine dinuclear copper(II) complexes with hxta5- ligands [H5hxta = N,N'-(2-hydroxy-1,3-xylylene)-bis-(N-carboxymethylglycine)]: [Cu2(MeO-hxtaH)(H2O)2] x 4H2O (1), [Na(micro-H2O)2(H2O)6][Cu2(Cl-hxta)(H2O)3]2 x 6H2O (2), [Cu(H2O)6][Cu2(Me-hxta)(H2O)2](NO3) x 2H2O (3), [Cu2(R-hxtaH)(H2O)3] x 3H2O [R = Cl (4), CH3 (5), and MeO (6)], [Cu2(MeO-hxtaH2)(micro-X)(CH3OH)] x 3CH3OH [X = Cl (7), Br (8)] and K5Na(micro-H2O)10[Cu2(micro-CO3)(Me-hxta)]2 x 4H2O (9), have been synthesized and structurally characterized. In complexes 4-7, the dinuclear units are linked via novel pairwise supramolecular interactions involving the ligand carboxylate groups. The intra- and intermolecular magnetic interactions have been quantified, and the coupling constants have been related to the structural geometries.

Synthesis of novel types of copper-bipyridyl porphyrins and characterization of their interactions and reactivity with DNA

The inherent ability to interact with DNA makes cationic metallo-porphyrins attractive targets as antitumor drugs. Many studies describe their interaction with DNA and the mechanism by which they induce DNA cleavage. Since porphyrins can be used as anchors for chemically reactive groups, it is possible to modify them to generate a family of compounds with specific functions. In the present work, we used chemical groups such as copper-bipyridinium (Cu-bpy), which hydrolyze phosphodiester bonds, and a porphyrin core to synthesize two novel Cu(2)-bpy-porphyrins. Their interactions with DNA have been characterized using classic spectroscopic methods, and their oxidative and hydrolytic reactivity toward supercoiled plasmid DNA has been studied in vitro. Our results show that Cu(2)-bpy-porphyrins interact with DNA via external association and intercalation and that their ability to cleave DNA and the mechanisms depends on the experimental conditions.

Geometry-dependent phosphodiester hydrolysis catalyzed by binuclear copper complexes

Two isomeric binuclear ligands PBTPA and MBTPA and their copper(II) complexes were prepared and examined for hydrolysis of a model phosphodiester substrate: bis(p-nitrophenyl)phosphate. A bell-shaped pH vs rate profile, which is in agreement with one mechanism proposed for bimetallonucleases/phosphatases, was observed for the binuclear complex of copper(II) and PBTPA. At pH 8.4, a maximum rate of 1.14 x 10(-6) s(-1)--more than 10(4)-fold over uncatalyzed reactions--was achieved. However, the analogous complex of MBTPA did not show significant rate enhancement. The binuclear complex of copper(II) and PBTPA also showed 10-fold acceleration over mononuclear complex of copper(II) and tris(2-pyridylmethyl)amine (TPA) catalyzed reaction. A phage phiX174 DNA assay showed that the complex of copper(II) and PBTPA promoted supercoiled phage phiX174 DNA relaxation under both aerobic and anaerobic conditions, in contrast to the hydrolytic inactivity of the mononuclear complex of copper(II) and TPA.

Sequence selective hydrolysis of linear DNA using conjugates of Zr(IV) complexes and peptide nucleic acids

A series of conjugates of peptide nucleic acids (PNA) and Zr(IV) complexes was prepared. Their ability to hydrolyze DNA was tested using MALDI-TOF mass spectrometry and HPLC. The most efficient artificial restriction enzyme found, PNA conjugate with Zr(IV) complex of tris(hydroxymethyl)-aminomethane, cleaves DNA targets sequence selectively in close proximity to the Zr(IV) complex. It was demonstrated that cleavage products are substrates of terminal transferase.

DNA strand scission by a Cu(I).adenylated polymeric template: preliminary mechanistic and recycling studies

Cleavage of a model phosphate ester and supercoiled plasmid DNA by a Cu(I).adenylated polymer template and preliminary mechanistic investigations are reported. A novel paradigm for the design of recyclable nucleolytic reagents allowing multiple use of this catalyst is also demonstrated