Insights on nuclease mechanism: the role of proximal ammonium group on phosphate esters cleavage.

The role of remotely located ammonium groups in the active site of many phosphate-cleaving enzymes is investigated by using model systems thus providing mechanistic hints to a still unsolved problem.

Phosphate diester and DNA hydrolysis by a multivalent, nanoparticle-based catalyst.

2-nm gold nanoclusters coated with Zn(II) complexes bearing auxiliary hydrogen bond donors act as multivalent catalysts capable of promoting the hydrolysis of model phosphate diesters with exceptional activity and inducing DNA double strand cleavage.

Self-organized fluorescent nanosensors for ratiometric Pb2+ detection.

Silica nanoparticles (60 nm diameter) doped with fluorescent dyes and functionalized on the surface with thiol groups have been proved to be efficient fluorescent chemosensors for Pb2+ ions. The particles can detect a 1 microM metal ion concentration with a good selectivity, suffering only interference from Cu2+ ions. Analyte binding sites are provided by the simple grafting of the thiol groups on the nanoparticles. Once bound to the particles surface, the Pb2+ ions quench the emission of the reporting dyes embedded. Sensor performances can be improved by taking advantage of the ease of production of multishell silica particles. On one hand, signaling units can be concentrated in the external shells, allowing a closer interaction with the surface-bound analyte. On the other, a second dye can be buried in the particle core, far enough from the surface to be unaffected by the Pb2+ ions, thus producing a reference signal. In this way, a ratiometric system is easily prepared by simple self-organization of the particle components.

Silica nanoparticles for fluorescence sensing of Zn(II): exploring the covalent strategy.

Silica nanoparticles (about 15 nm diameters), which contain a derivative of 6-methoxy-8-(p-toluensulfonamido)-quinoline (TSQ) as a Zn(II) fluorescent probe covalently linked to the silica network, were prepared and studied as Zn(II) fluorescent chemosensors. The systems selectively detect Zn(II) ions in water rich solutions with a submicromolar sensitivity: 0.13 microM concentrations of Zn(II) can be measured with the only interference of Cu(II) and Cd(II) ions. Compared with free TSQ, the nanoparticles based systems have the advantage that they can be employed in aqueous solutions without aggregation problems while at the same time, they maintain a similar Zn(II) affinity and sensing ability. Addition of a second, substrate insensitive, fluorophore to the particles leads to the realization of a ratiometric sensor.

Mimicking enzymes: cooperation between organic functional groups and metal ions in the cleavage of phosphate diesters.

A series of ligands derived from the bis-2-pyridinylmethylamine structure, which bear either additional hydroxyl or aromatic amino groups, were prepared and their Zn(II) complexes were studied as catalysts for the cleavage of bis-p-nitrophenyl phosphate (BNP) and 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) diesters. A comparative kinetic study indicated that the insertion of organic groups, capable of acting as nucleophiles or as hydrogen-bond donors, substantially increases the hydrolytic activity of the metal complex. Dissection of the effects of the individual groups revealed that the increase in reactivity can reach up to three orders of magnitude. The improved efficiency of the systems studied, combined with the benefits resulting from the low pK(a) value of the active nucleophile, result in an acceleration of the BNP cleavage at pH 7 of six orders of magnitude. The pH-dependent reactivity profiles follow a bell-shaped curve and the maximum reactivity is observed at pH 9. The mechanism of the reactions and the structure of the complexes were investigated in detail by means of kinetic analysis, NMR spectroscopy experiments, and theoretical calculations. The reactivity of the complexes that cleave HPNP closely resembles the reactivity observed for BNP, but the accelerations achieved are lower as a result of different reaction mechanisms.

Size effect on the fluorescence properties of dansyl-doped silica nanoparticles.

We present here the study of the photophysical properties of new dye-doped silica nanoparticles (DDNs) bearing dansyl fluorescent derivatives covalently linked to the silica matrix. The described experimental evidences show how the different location of the chromophores induces great changes in their photophysical behavior, suggesting that fluorophores located near the surface of the nanoparticles have a very different behavior with respect to the internal molecules. These latter ones, in fact, are shielded from the solvent and have a strong blue emission, while those at the periphery interact with the solvent and show a weaker red-shifted emission. As a consequence, the fluorescence properties of these nanoparticles are an average between the characteristics of the two different families of dyes. The relative amount of fluorophores located in the two compartments can be controlled simply by changing the size since, from our results, the thickness of the solvent permeable layer is not relevantly affected by the diameter of the nanoparticles. It is noteworthy that the fluorophores located in the outer shell exhibit very peculiar features: they are sensitive and interact with small molecules such as solvent molecules but, at the same time, they are not accessible to big receptor species such as beta-cyclodextrins. Such results indicate that most of the solvent-sensitive dansyl moieties are located within pores large enough to only accommodate solvent but not big molecules as cyclodextrins, giving precious insight on the morphology of the nanoparticles.

Self-assembled fluorescent chemosensors.

Self-assembling and self-organizing methodologies are powerful tools for the "bottom-up" approach for the realization of complex structure with functional properties. Recently, this concept has been extended to the design of fluorescent chemosensors providing new exciting potentialities for the development of innovative sensing systems. This Concept Article deals mainly with this new approach and discusses its evolution, applications, and limitations.

Turning fluorescent dyes into Cu(II) nanosensors.

There is great interest in the self-organization of the proper subunits as a new strategy for the realization of fluorescent chemosensors. In this article, it is shown that commercially available fluorescent dyes, functionalized with triethoxysilane moieties, can be converted into fluorescent chemosensors by simple inclusion into silica nanostructures. Dye-doped silica nanoparticles and thin films detect Cu(II) ions in the micromolar range by the quenching of fluorescence emission. The different response toward Zn(II), Ni(II), and Co(II) metal ions was also investigated and is reported. The self-organization of the silica structures leads, at the same time, to the formation of metal ion binding sites as well as to the linking of a fluorescent reporter in their proximity. Structural features of the materials, particularly particle size and network porosity, strongly affect their ability to act as fluorescent sensors.

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.

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.

Multiple functional group cooperation in phosphate diester cleavage promoted by Zn(II) complexes.

Zn(II) complexes bearing multiple auxiliary organic groups greatly accelerate the cleavage of a phosphate diester.

One-pot synthesis of cyanuric acid-bridged porphyrin-porphyrin dyads.

Stepwise amination of cyanuric chloride (1) with 5-(4-aminophenyl)-10,15,20-triphenylporphyrin (2) and/or its zinc(II) complex (3) enables the synthesis of porphyrin-porphyrin dyads with predetermined free base-free base forms or free base-zinc and zinc-zinc metalation states. Furthermore, the use of aminopropyl-silanized silica gel as a scavenger for unwanted byproducts allowed the one-pot synthesis of title porphyrin compounds in high yield and purity with minimum use of preparative column chromatography.

Toward efficient Zn(II)-based artificial nucleases.

A series of cis-cis-triaminocyclohexane Zn(II) complex-anthraquinone intercalator conjugates, designed in such a way to allow their easy synthesis and modification, have been investigated as hydrolytic cleaving agents for plasmid DNA. The ligand structure comprises a triaminocyclohexane platform linked by means of alkyl spacers of different length (from C(4) to C(8)) to the anthraquinone group which may intercalate the DNA. At a concentration of 5 microM, the complex of the derivative with a C(8) alkyl spacer induces the hydrolytic stand scission of supercoiled DNA with a rate of 4.6 x 10(-6) s(-1) at pH 7 and 37 degrees C. The conjugation of the metal complex with the anthraquinone group leads to a 15-fold increase of the cleavage efficiency when compared with the anthraquinone lacking Zn-triaminocyclohexane complex. The straightforward synthetic procedure employed, allowing a systematic change of the spacer length, made possible to gain more insight on the role of the intercalating group in determining the reactivity of the systems. Comparison of the reactivity of the different complexes shows a remarkable increase of the DNA cleaving efficiency with the length of the spacer. In the case of too-short spacers, the advantages due to the increased DNA affinity are canceled due to the incorrect positioning of the reactive group, thus leading to cleavage inhibition.

Synthesis of 6I-amino-6I-deoxy-2I-VII,3I-VII-tetradeca-O-methyl-cyclomaltoheptaose.

The preparation of 6(I)-amino-6(I)-deoxy-2(I-VII),3(I-VII)-tetradeca-O-methyl-cyclomaltoheptaose is reported. Two different routes (A and B), both starting from beta-cyclodextrin (betaCD), have been examined. Route A involved: (i) synthesis of heptakis(6-O-tert-butyldimethylsilyl)-betaCD from betaCD; (ii) permethylation of the secondary hydroxyl groups with methyl iodide and sodium hydride; (iii) desilylation of the primary hydroxyls with ammonium fluoride; (iv) monotosylation at O-6 position of per-(2,3-O-methyl)-betaCD; (5) nucleophilic replacement of the tosyl group with azide anion; (v) reduction of the azido group by catalytic transfer hydrogenation using hydrazine hydrate in the presence of Pd/C in methanol/water. Route B started from the known 6(I)-monoazido-6(I)-monodeoxy-beta-CD (two steps from beta-CD) and entailed: (i) protection of the remaining primary hydroxyls using tert-butyldimethylsilylchloride (TBDMSCl); (ii) exhaustive methylation of the secondary hydroxyls with methyl iodide and sodium hydride; (iii) removal of the TBDMS protecting groups with ammonium fluoride; (iv) reduction of the azido group as above. Route A was found to be less convenient than Route B due to the inherent difficulty of controlling the monotosylation of per-(2,3-O-methyl)-betaCD.

The ligand effect on the hydrolytic reactivity of Zn(II) complexes toward phosphate diesters.

The catalytic effects of the Zn(II) complexes of a series of poliaminic ligands in the hydrolysis of the activated phosphodiesters bis-p-nitrophenyl phosphate (BNP) and 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) have been investigated. The reactions show first-order rate dependency on both substrate and metal ion complex and a pH dependence which is diagnostic of the acid dissociation of the reactive species. The mechanism of the metal catalyzed transesterification of HPNP has been assessed by solvent isotopic kinetic effect studies and involves the intramolecular nucleophilic attack of the substrate alcoholic group, activated by metal ion coordination. The intrinsic reactivity of the different complexes is controlled by the nature and structure of the ligand: complexes of tridentate ligands, particularly if characterized by a facial coordination mode, are more reactive than those of tetradentate ligands which can hardly allow binding sites for the substrate. In the case of tridentate ligands that form complexes with a facial coordination mode, a linear Brønsted correlation between the reaction rate (log k) and the pK(a) of the active nucleophile is obtained. The beta(nuc) values are 0.75 for the HPNP transesterification and 0.20 for the BNP hydrolysis. These values are indicated as the result of the combination of two opposite Lewis acid effects of the Zn(II) ion: the activation of the substrate and the efficiency of the metal coordinated nucleophile. The latter factor apparently prevails in determining the intrinsic reactivity of the Zn(II) complexes.

A fluorescence nanosensor for Cu2+ on silica particles.

A fluorescence nanosensor for Cu2+ ions has been obtained by surface functionalization of silica particles with trialkoxysilane derivatized ligand and fluorescent dye.

Efficient sensitized photooxygenation in water by a porphyrin-cyclodextrin supramolecular complex.

[reaction: see text] The 2:1 inclusion complex between (2,3,6-tri-O-methyl)-beta-cyclodextrin (TMbetaCD) and 5,10,15,20-tetrakis(4-sulfonatophenyl)-porphyrin (TPPS(4)) behaves as a supramolecular sensitizer in water providing photooxygenation with turnover numbers up to 30,000 with a very minor sensitizer bleaching (<10%). The protocol, which employs only 4 equiv of the cyclodextrin additive with respect to the porphyrin sensitizer (5 x 10(-7) M), leads to high yield oxidation of model biomolecules such as l-methionine methyl ester and uracil and is also effective for phenol degradation in aqueous solution.

Capillary zone electrophoresis study of cyclodextrin--lipoic acid host-guest interaction.

Lipoic acid is a naturally occurring compound which is being widely investigated for its therapeutic effects in the treatment or prevention of a variety of diseases associated with oxidative injury, particularly diabetes. The diversity of therapeutic applications of lipoic acid requires an appropriate formulation to control its bioavailability, site-targeting delivery and to overcome its inherent chemical instability. In this regard, cyclodextrins (CDs) are ideally suitable due to their well-documented ability to include in their cavity proper guest molecules and protect them from physical or chemical damages. Lipoic acid forms 1:1 inclusion complexes with betaCD as shown in a previous report of an extended investigation that also indicated the suitability of capillary zone electrophoresis (CZE) for the study of such host-guest interactions. In view of these possible applications, we extended the CZE analysis to determine the strength of binding, in a pH 9 phosphate buffer, of lipoic acid with other CD derivatives such as alphaCD, gammaCD and the alkylated derivatives of betaCD, namely (2-hydroxypropyl)-beta-CD (HPbetaCD), and heptakis(2,3,6-tri-O-methyl)-beta-CD (TMbetaCD). Once established that the easily available betaCD is the most suitable receptor for lipoic acid, we set up and here describe a simple and reliable procedure for the quantitative determination of lipoic acid in commercial dietary supplement tablets containing also other active substances and excipients.

Zinc(II) as an allosteric regulator of liposomal membrane permeability induced by synthetic template-assembled tripodal polypeptides.

Three copies of peptide sequences from the peptaibol family, known to affect the permeability of the lipid bilayer of membranes, were connected to tris(2-aminoethyl)amine (TREN), a tripodal metal ion ligand, to prepare functional peptides capable of modifying the permeability of liposomal membranes. Some of the resulting tripodal polypeptide derivatives are very effective in promoting carboxyfluorescein (CF) leakage from CF-loaded unilamellar vesicles composed of a 70:30 phosphatidylcholine/cholesterol blend. The activity of these novel compounds was shown to be tunable upon metal ion coordination of the TREN subunit; the tripodal apopeptide was far more effective than its ZnII complex. Leakage experiments showed that a minimum number of five amino acids per peptide chain is required to form active systems. A mechanism is proposed in which the ZnII ion changes the conformation of the template from extended to globular and thus acts as an allosteric regulator of the activity of the systems. Molecular modeling studies indicate that when the three peptide chains are connected to the template in the extended conformation, the resulting tripodal polypeptide is able to span across the membrane, thus allowing the formation of permeable channels made of a cluster of molecules. The same change of conformation induces, to some extent, fusion of the membranes of different liposomes.

Fluorescence sensing of ionic analytes in water: from transition metal ions to vitamin B13.

The fluorescence chemosensor ATMCA has been realised by appending an anthrylmethyl group to an amino nitrogen of TMCA (2,4,6-triamino-1,3,5-trimethoxycyclohexane), a tripodal ligand selective for divalent first-row transition metal ions in water. The ATMCA ligand can act as a versatile sensor for ZnII and CuII ions. Its sensing ability can be switched by simply tuning the operating conditions. At pH 5, ATMCA detects copper(II) ions in aqueous solutions by the complexation-induced quenching of the anthracene emission. Metal ion concentrations < 1 microM can be readily detected and very little interference is exerted by other metal ions. At pH 7, ATMCA signals the presence of ZnII ions at concentrations < 1 microM by a complexation-induced enhancement of the fluorescence. Again the sensor is selective for ZnII over several divalent metal ions, with the exception of CuII, CoII and HgII. Most interestingly, the [ZnII(atmca)]2+ complex can act as a fluorescence sensor for specific organic species, notably selected dicarboxylic acids and nucleotides, by the formation of ternary ligand/zinc/substrate complexes. The oxalate anion is detected in concentrations <0.1 mM; however, no effects on the system's fluorescence is observed in the presence of monocarboxylic acids and long-chain dicarboxylic acids. Among the nucleotides, those containing an imide or amide function are readily detected and an unprecedented high sensitivity for guanine derivatives allows the determination of this nucleotide for 0.05-0.5 mM solutions. Moreover, [ZnII(atmca)]2+ is a very effective and selective sensor in the case of vitamin B13 (orotic acid) in sub-micromolar concentrations. The operative features of the systems investigated are also clearly suitable for intracellular analyses. The factors at the source of organic substrate recognition, here briefly discussed, are of paramount importance for further developments in the applicability of these sensing systems.