Binding of Al(iii) to synthetic RNA and metal-mediated strand aggregation.

Over the last few years, focused interest in aluminum has been heightened by recent studies regarding its health effects. Its possible relation with chronic diseases makes it convenient to address more in depth the reactivity of aluminum with biologically relevant molecules. The present work investigates the interaction of the aluminum ion with two synthetic RNAs, poly(rA) and poly(rU), through a detailed thermodynamic and kinetic study. The trivalent aluminum ion was kept in solution by complexation with the cacodylate anion, even at neutral pH, thus making the study with biological molecules feasible. The results obtained by spectrophotometry, circular dichroism, viscometry and thermal stability measurements indicate that aluminium strongly interacts with single and duplex RNA structures. The kinetic experiments point out that, even though cacodylate is required to keep the metal in solution, it actually inhibits the reaction of aluminum with RNA as it converts the metal into an unreactive dimer species. Notably, further interaction occurred in an excess of the aluminum/cacodylate complex, inducing aggregation of single-stranded RNAs. An analysis of the kinetic data has shown that the modes of aggregation of the two RNAs differ and such a difference can be ascribed to the diverse polynucleotide secondary structures. The observed stabilization of multiple-stranded systems by aluminum can serve as a model for future studies due to the interest aroused by this metal in the study of non-canonical nucleic acid structures.

Stabilization of Al(III) solutions by complexation with cacodylic acid: speciation and binding features.

Aluminium ions are believed to play a role in a number of neurological and skeletal disorders in the human body. The study of the biological processes and molecular mechanisms that underlie these pathological disorders is rendered a difficult task due to the wide variety of complex species that result from the hydrolysis of Al(3+) ions. In addition, this ion displays a pronounced tendency to precipitate as a hydroxide, so certain complexing agents should be envisaged to stabilize Al(III) solutions in near physiological conditions. In this work, we show that the common buffer cacodylic acid (dimethylarsinic acid, HCac) interacts with Al(III) to give stable complexes, even at pH 7. After preliminary analyses of the speciation of the metal ion and also of the ligand, a systematic study of the formation of different Al/Cac complexes at different pH values has been conducted. UV-Vis titrations, mass spectrometry NMR measurements and DTF calculations were performed to enlighten the details of the speciation and stoichiometry of Al/Cac complexes. The results altogether show that Al/Cac dimer complexes prevail, but monomer and trimer forms are also present. Interestingly, it was found that cacodylate promotes the formation of such relatively simple complexes, even under conditions where the polymeric form, Al13O4(OH)24(7+), should predominate. The results obtained can help to shed some light into the reactivity of aluminium ions in biological environments.

Mg(II) and Ni(II) induce aggregation of poly(rA)poly(rU) to either tetra-aggregate or triplex depending on the metal ion concentration.

The ability of magnesium(II) and nickel(II) to induce dramatic conformational changes in the synthetic RNA poly(rA)poly(rU) has been investigated. Kinetic experiments, spectrofluorometric titrations, melting experiments and DSC measurements contribute in shedding light on a complex behaviour where the action of metal ions (Na(+), Mg(2+), Ni(2+)), in synergism with other operators as the intercalating dye coralyne and temperature, all concur in stabilising a peculiar RNA form. Mg(2+) and Ni(2+) (M) bind rapidly and almost quantitatively to the duplex (AU) to give a RNA/metal ion complex (AUM). Then, by the union of two AUM units, an unstable tetra-aggregate (UAUA(M2)*) is formed which, in the presence of a relatively modest excess of metal, evolves to the UAUM triplex by releasing a single AM strand. On the other hand, under conditions of high metal content, the UAUA(M2)* intermediate rearranges to give a more stable tetra-aggregate (UAUA(M2)). As concerns the role of coralyne (D), it is found that D strongly interacts with UAUA(M2). Also, in the presence of coralyne, the ability of divalent ions to promote the transition of AUD into UAUD is enhanced, according to the efficiency sequence [Ni(2+)]≫[Mg(2+)]≫[Na(+)].

Aggregation features and fluorescence of Hoechst 33258.

The functionality of the bisbenzimide Hoechst 33258 in solution has been largely exploited in the quantification of DNA. Understanding of its behavior is essential to promote its widespread application and learning of biological processes. A detailed study of the dimerization process of the fluorescent blue dye Hoechst 33258 is carried out by isothermal titration calorimetry, absorbance, fluorescence, differential scanning calorimetry and T-jump kinetic measurements. The dimer/monomer ratio depends on the dye concentration and the ionic strength. The dimerization constant determined under physiological conditions (pH = 7.0; I = 0.10 M), KD = 3 × 10(4) M(-1), conveys that only micromolar concentrations of the dye can ensure reasonably high amounts of the monomer species in solution. For instance, for 10 µM dye content, the dimer prevails for I > 0.08 M, whereas the monomer is observed at low ionic strength, a key issue to be elucidated as long as the dimer species is more fluorescent than the monomer and the fluorescence intensity strongly relies on the ionic strength and the dye concentration.

The mechanism of the Cu²âº[12-MCCu(Alaha)-4] metallacrown formation and lanthanum(III) encapsulation.

A kinetic, calorimetric, mass spectrometry and EPR study has been performed on the formation of the metallacrown Cu(2+)[12-MCCu(Alaha)-4] from Cu(ii) and α-alaninehydroxamic acid (H2L). The acidity range where Cu(2+)[12-MCCu(Alaha)-4] is stable lies between pH 3.5 and 6.0. For pH values below that range the complex CuHL(+) is the prevailing species. This species plays a fundamental role in the formation of Cu(2+)[12-MCCu(Alaha)-4]. Actually, depending on the Cu(II)/H2L ratio and on pH, it can originate a dimer Cu2(HL)2(2+) or a dinuclear complex Cu2L(2+). Both species constitute the nuclei necessary for a further oligomerisation reaction which ends when the crown is formed. The kinetics of Cu(2+)[12-MCCu(Alaha)-4] formation is biphasic. Under conditions of Cu(II) excess the fast phase leads to formation of Cu2L(2+). The slow phase is interpreted in terms of a sequential addition of monomers (CuHL(+)) to the Cu2L(2+) nucleus to form the crown. The interaction of La(III) with Cu(2+)[12-MCCu(Alaha)-4] has also been investigated. The system displays a biphasic behaviour; in the first phase the intermediate complex Cu[12-MCCu(Alaha)-4]La is formed which, in excess of ligand, evolves towards the larger metallacrown La(3+)[15-MCCu(Alaha)-5]. The reaction mechanisms of the two investigated systems are discussed.

RNA triplex-to-duplex and duplex-to-triplex conversion induced by coralyne.

Spectrophotometric, circular dichroism, calorimetric, displacement assay and kinetic analyses of the binding of the fluorescent dye coralyne to poly(A)2poly(U) have served to enlighten the ability of the dye to produce dramatic changes in the RNA structure. The sets of data assembled convey that coralyne is able to induce the triplex-to-duplex conversion and also the duplex-to-triplex conversion according to a non-reversible cycle governed by temperature, provided that the [dye]/[polymer] ratio (CD/CP) is maintained constant above unity. Alternatively, at room temperature the triplex is formed at (roughly) CD/CP < 1 and the duplex at CD/CP > 1.

An investigation of the photophysical properties of minor groove bound and intercalated DAPI through quantum-mechanical and spectroscopic tools.

The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI) is a dye known to interact with polynucleotides in a non-univocal manner, both intercalation and minor groove binding modes being possible, and to specifically change its photophysical properties according to the different environments. To investigate this behavior, quantum-mechanical calculations using time-dependent density functional theory (TDDFT), coupled with polarizable continuum and/or atomistic models, were performed in combination with spectroscopic measurements of the probe in the different environments, ranging from a homogeneous solution to the minor groove or intercalation pockets of double stranded nucleic acids. According to our simulation, the electronic transition involves a displacement of the electron charge towards the external amidine groups and this feature makes the absorption energies very environment-sensitive while a much smaller sensitivity is seen in the fluorescence energies. Moreover, the calculations show that the DAPI molecule, when minor groove bound to the nucleic acid, presents both a reduced geometrical flexibility because of the rigid DNA pocket and a reduced polarization due to the very "apolar" microenvironment. All these effects can be used to better understand the observed enhancement of the fluorescence, which makes it an excellent marker for DNA.

Mechanism of Ni2+ and NiOH+ interaction with hydroxamic acids in SDS: evaluation of the contributions to the equilibrium and rate parameters in the aqueous and micellar phase.

The equilibria and kinetics (stopped-flow) of the binding of Ni(II) to salicylhydroxamic acid (SHA) and phenylbenzohydroxamic acid (PBHA) have been investigated in aqueous solutions containing SDS micelles. The two ligands are fairly distributed between the two pseudophases present, so the binding reaction occurs in both phases. The contributions to the total reaction from each phase has been evaluated, following a procedure where use is made of the experimentally determined partition coefficients of the reactants involved. The mechanism of the reaction occurring on the micelle surface has been derived and comparison with the mechanism in water shows that the step Ni(2+) + HL ⇄ NiHL(2+) is operative in both pseudophases, whereas the step Ni(2+) + L(-)⇄ NiL(+), which is operative in water, is replaced in SDS by the step NiOH(+) + HL ⇄ NiL(+). The analysis of the equilibrium and of the kinetic data enabled the evaluation of the equilibrium and the rate constants of the individual steps taking part in the binding process over the micelle surface. Interestingly, the first hydrolysis constant of the Ni(H(2)O)(6)(2+) ion in SDS is more than two orders of magnitude higher than in water. The agreement between the equilibrium constants derived from kinetics and those obtained by static measurements confirms the validity of the proposed mechanism.

The fluorophore 4',6-diamidino-2-phenylindole (DAPI) induces DNA folding in long double-stranded DNA.

DAPI (4',6-diamidino-2-phenylindole) is a widely used fluorescent dye, whose complicated binding features to DNAs and RNAs have been the object of debates and are still not fully understood. In this study, different approaches were employed, including binding equilibrium measurements (spectrofluorometry), melting experiments (spectrophotometry), viscometric measurements, circular dichroism, and T-jump kinetic analyses; all data concur in shedding light on the complex mechanistic aspects of the binding mode of DAPI to natural DNA. Conditions are found that induce the mode of the DAPI/DNA interaction to change from groove binding to intercalation. Moreover, it is observed, for the first time, that DAPI is able to induce the formation of a rather compact polymer-dye adduct under particular conditions. The results suggest that this form is a folded or coiled DNA structure stabilized by DAPI dye bridges.

The mode of binding ACMA-DNA relies on the base-pair nature.

A thermodynamic and kinetic study on the mode of binding of 9-amino-6-chloro-2-methoxi-acridine (ACMA) to poly(dA-dT)·poly(dA-dT) and poly(dG-dC)·poly(dG-dC) has been undertaken at pH = 7.0 and I = 0.1 M. The spectrophotometric, kinetic (T-jump), circular dichroism, viscometric and calorimetric information gathered point to formation of a fully intercalated ACMA complex with poly(dA-dT)·poly(dA-dT) and another one only partially intercalated (7%) with poly(dG-dC)·poly(dG-dC). The ACMA affinity with the A-T bases was higher than with the G-C bases. The two polynucleotide sequences give rise to external complexes when the ACMA concentration is raised, namely, the electrostatic complex poly(dA-dT)·poly(dA-dT)-ACMA and the major groove binding complex poly(dG-dC)·poly(dG-dC)-ACMA. A considerable quenching effect of the ACMA fluorescence is observed with poly(dA-dT)·poly(dA-dT), ascribable to face-to-face location in the intercalated A-T-ACMA base-pairs. The even stronger effect observed in the presence of poly(dG-dC)·poly(dG-dC) is related to the guanine residue from on- and off-slot ACMA positions.

ACMA (9-amino-6-chloro-2-methoxy acridine) forms three complexes in the presence of DNA.

The interaction of ACMA (9-amino-6-chloro-2-methoxy acridine) (D) with DNA (P) has been studied by absorbance, fluorescence, circular dichroism, spectrophotometry, viscometry and unwinding electrophoresis. A T-jump kinetic study has also been undertaken. The experimental data show that, totally unlike other drugs, ACMA is able to form with DNA three complexes (PD(I), PD(II), PD(III)) that differ from each other by the characteristics and extent of the binding process. The main features of PD(I) fulfil the classical intercalation pattern and the formation/dissociation kinetics have been elucidated by T-jump techniques. PD(II) and PD(III) are also intercalated species but, in addition to the dye units lodged between base pairs, they also bear dye molecules externally bound, more in PD(III) relative to PD(II). A reaction mechanism is put forward here. Comparison between absorbance, fluorescence and kinetic experiments has enabled us to determine the binding constants of the three complexes, namely (6.5 ± 1.1) × 10(4) M(-1) (PD(I)), (5.5 ± 1.5) × 10(4) M(-1) (PD(II)) and (5.7 ± 0.03) × 10(4) M(-1) (PD(III)). The Comet assay reveals that the ACMA binding to DNA brings about genotoxic properties. The mutagenic potential studied by the Ames test reveals that ACMA can produce frameshift and transversion/transition mutations. ACMA also is able to produce base-pair substitution in the presence of S9 mix. Moreover, the MTT assays have revealed cytotoxicity. The biological effects observed have been rationalized in light of these features.

Route to metallacrowns: the mechanism of formation of a dinuclear iron(III)-salicylhydroxamate complex.

The equilibria and the kinetics of the binding of Iron(III) to salicylhydroxamic (SHA) and benzohydroxamic (BHA) acids have been investigated in aqueous solution (I = 1 M (HClO(4)/NaClO(4)), T = 298 K) using spectrophotometric and stopped-flow methods. Whereas Iron(III) forms a 1:1 complex (ML) with BHA, it forms both ML and M(2)L complexes with SHA. The presence of M(2)L in aqueous medium is corroborated by FTIR measurements. The reactive form of Iron(III) is the hydrolyzed species FeOH(2+), which binds to the O,O site in ML and to the O,O and O(P),N (P = phenolate) sites in M(2)L, inducing full deprotonation of the latter. The reaction pathway is discussed in terms of a multistep mechanistic scheme in which the metal-ligand interaction is coupled to hydrolysis and self-aggregation steps of Iron(III). The observation and characterization of M(2)L as a stable species is important because it contains the -Fe-O-N-Fe- sequence, which constitutes the repetitive motif of the SHA-based metallacrown ring and provides the rationale for 12-MC-4 metallacrowns. In the framework of this study, the kinetics of the Iron(III) dimerization and trimerization have also been investigated using the stopped-flow method to perform dilution jumps. The reaction scheme put forward involves two parallel steps (FeOH(2+) + FeOH(2+) and Fe(3+) + FeOH(2+)) that lead to formation of the Fe(2)(OH)(2)(4+) dimer and a slower step (FeOH(2+) + Fe(2)(OH)(2)(4+)) to form the trimer species. The kinetics of the last step have been investigated here for the first time, and the results deduced indicate that, of the two possible trimer structures reported in the literature, Fe(3)(OH)(3)(6+) and Fe(3)(OH)(4)(5+), the latter prevails by far.

Thiazole orange (TO) as a light-switch probe: a combined quantum-mechanical and spectroscopic study.

A Density Functional Theory (DFT) study of the absorbance and fluorescence emission characteristics of the cyanine thiazole orange (TO) in solution and when intercalated in DNA was carried out in combination with spectrophotometric and spectrofluorometric experiments under different conditions (temperature, concentration, solvent viscosity). T-jump relaxation kinetics of the TO monomer-dimer conversion enabled the thermodynamic parameters of this process to be evaluated. The overall data collected provided information on the features of the "light-switch" by the fluorescent TO and the comparison between experimental and calculated photo-physical properties allowed us to explain and rationalize both shifts and quenching/enhancing effects on fluorescence due to solvation, dimerisation and intercalation in the DNA.

Synthesis, characterization, DNA interaction and potential applications of gold nanoparticles functionalized with Acridine Orange fluorophores.

Two new water-soluble gold nanoparticles (AO-TEG-Au and AO-PEG-Au NPs) are prepared and characterized. They are stabilized by thioalkylated oligoethylene glycols and functionalized with fluorescent Acridine Orange (AO) derivatives. Despite the different core sizes (11.8 and 3.9 nm respectively) and shell composition, they are both well dispersed and are stable in water, even if some self-aggregation is observed in the case of AO-TEG-Au NPs. However, AO-PEG-Au NPs show much lower emission efficiency with respect to AO-TEG-Au NPs. Spectrophotometric and spectrofluorometric experiments indicate that both types of nanoparticle are able to bind to calf thymus DNA, either by external binding or partial intercalation. Preliminary FACS flow cytometry tests seem to indicate that the AO-TEG-Au nanoparticle is able to cross the cell membrane where it is absorbed by Chinese hamster ovary (CHO) cells at the picomolar concentration level.

DNA binding of a proflavine derivative bearing a platinum hanging residue.

New platinum(II) complex of 3,6-diamine-9-[6,6-bis(2-aminohethyl)-1,6-diaminohexyl]acridine, AzaPt, has been synthesised and characterised. Behaviour of AzaPt in solution (protonation and possible self-aggregation phenomena) has been investigated by spectral methods (absorbance and fluorescence) at I=0.1M and 25°C, and the equilibrium parameters of binding to calf thymus DNA have been established. Two different modes of DNA binding by the complex were detected, which depend on the polymer to dye molar ratio (P/D). At relatively low P/D values the mode was interpreted as binding by the polyamine residue external to the base pairs, while at high P/D values the binding corresponds to intercalation of the proflavine residue. Such interpretation is supported by the observed salt effect on binding and the temperature variation of the binding constants, which allowed estimating the ΔH and ΔS values contributions. Spectrophotometric analysis of the long time range binding revealed that AzaPt is involved in a slow reaction, interpreted as an attack by the platinum ion on the nucleobases. The time constant for such interaction was calculated and found to be the same order of magnitude as for processes responsible for the action of anti-tumour drugs that do covalently bind to polynucleotides.

Left-handed DNA: intercalation of the cyanine thiazole orange and structural changes. A kinetic and thermodynamic approach.

The conditions under which different structures of left-handed DNA (poly(dG-me(5)dC)·poly(dG-me(5)dC)) can exist are investigated by spectrofluorometric, spectrophotometric, circular dichroism and calorimetric measurements and the kinetics of the transformations are analysed. The effects of temperature, salt and ethanol content on the transitions are also studied. The left-handed structure obtained by addition of either Mg(2+) ions or EtOH corresponds to Z-DNA, whereas the structure obtained using the mixture Mg(2+)/EtOH corresponds to the aggregate Z*-DNA. Upon addition of the fluorescent cyanine Thiazole Orange (TO), the transition Z → B immediately starts, whereas Z*-DNA retains its left-handed configuration in the presence of TO provided that the ratio [dye]/[polymer] ≤ 0.1. The equilibria and kinetics of the TO binding to Z*-DNA are investigated under the above conditions using the T-jump technique. The reaction mechanism consists of two series steps, the first one being characterized by the formation of an external electrostatic complex and the second corresponding to the dye penetration between the base pairs. A comparison with the B-DNA/TO system is drawn.

DNA interaction with Ru(II) and Ru(II)/Cu(II) complexes containing azamacrocycle and dppz residues. A thermodynamic, kinetic and theoretical study.

Ru(ii) complexes that bring together the properties of the dppz (dipyrido[3,2-a:2',3'-c]phenazine) intercalating residue and the properties of metal-coordinating macrocycles (L = 4,4'-(2,5,8,11,14-pentaaza[15])-2,2'-bipyridilophane) have been synthesised and their protonation and affinity for copper(ii) was analysed. Ru(bpy)(dppz)L(2+) (D2(2+)) and Ru(dppz)(2)L(2+) (D3(2+)) were found to interact with DNA but the binding mode is not simple and its features strongly depend both on the ligand structure and on the [DNA]/[complex] ratio. Equilibrium measurements (spectrophotometric and spectrofluorometric titrations), kinetics (stopped-flow technique) and theoretical calculations all concur in suggesting that for the less hindered D2(2+) an important contribution of external binding, driven by dye-dye interactions, is operative, as revealed by the onset of positive cooperativity. On the contrary, for the bulkier D3(2+) complex dye-dye interactions are less effective, resulting in an intercalation process with lower dppz penetration within DNA slots. The Ru(bipy)(2)L(2+)(D1(2+))/DNA system was also analysed for comparison and helped in showing the non negligible contribution of the macrocycle to the binding process. The binding affinities of the macrocycle copper complexes for DNA are lower than those of their copper-free analogues only in the case of D1(2+), whereas an affinity enhancement in agreement with the charge increase upon copper coordination is observed for D2(2+) and D3(2+). Copper coordination produces complete loss of the cooperative behaviour in the case of D2(2+). Further mechanistic details are discussed.

Change of the binding mode of the DNA/proflavine system induced by ethanol.

The equilibria and kinetics of the binding of proflavine to poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT) were investigated in ethanol/water mixtures using spectrophotometric, circular dichroism, viscometric, and T-jump methods. All methods concur in showing that two modes of interaction are operative: intercalation and surface binding. The latter mode is favored by increasing ethanol and/or the proflavine content. Both static and kinetic experiments show that, concerning the poly(dG-dC).poly(dG-dC)/proflavine system, intercalation largely prevails up to 20% EtOH. For higher EtOH levels surface binding becomes dominant. Concerning the poly(dA-dT).poly(dA-dT)/proflavine system, melting experiments show that addition of proflavine stabilizes the double stranded structure, but the effect is reduced in the presence of EtOH. The DeltaH degrees and DeltaS degrees values of the melting process, measured at different concentrations of added proflavine, are linearly correlated, revealing the presence of the enthalpy-entropy compensation phenomenon (EEC). The nonmonotonicity of the "entropic term" of the EEC reveals the transition between the two binding modes. T-jump experiments show two relaxation effects, but at the highest levels of EtOH (>25%) the kinetic curves become monophasic, confirming the prevalence of the surface complex. A branched mechanism is proposed where diffusion controlled formation of a precursor complex occurs in the early stage of the binding process. This evolves toward the surface and/or the intercalated complex according to two rate-determining parallel steps. CD spectra suggest that, in the surface complex, proflavine is bound to DNA in the form of an aggregate.

Solvent effects on the kinetics of the interaction of 1-pyrenecarboxaldehyde with calf thymus DNA.

The kinetics of the interaction of a fluorescent probe, 1-pyrenecarboxaldehyde, with calf thymus DNA has been studied in different water/alcohol mixtures (ethanol, 2-propanol, and ter-butanol) at 25 degrees C, by using the stopped flow technique. The kinetic curves are biexponential and reveal the presence of two processes whose rates differ by about 1 order of magnitude on the time scale. The dependence of the reciprocal fast relaxation time on the DNA concentration is linear, whereas the concentration dependence of the reciprocal slow relaxation time tends to a plateau at high DNA concentrations. The simplest mechanism consistent with the kinetic results involves a simple two-step series mechanism reaction scheme. The first step corresponds to the formation of a precursor complex, (DNA/Py)(I), while the second one corresponds to full intercalation of the pyrene dye between the DNA base pairs. The values of the rate constants of both steps decrease as water activity decreases. The results have been discussed in terms of solvation of the species and changes in the viscosity of the solution.

New aspects of the interaction of the antibiotic coralyne with RNA: coralyne induces triple helix formation in poly(rA)*poly(rU).

The interaction of coralyne with poly(A)*poly(U), poly(A)*2poly(U), poly(A) and poly(A)*poly(A) is analysed using spectrophotometric, spectrofluorometric, circular dichroism (CD), viscometric, stopped-flow and temperature-jump techniques. It is shown for the first time that coralyne induces disproportionation of poly(A)*poly(U) to triplex poly(A)*2poly(U) and single-stranded poly(A) under suitable values of the [dye]/[polymer] ratio (C(D)/C(P)). Kinetic, CD and spectrofluorometric experiments reveal that this process requires that coralyne (D) binds to duplex. The resulting complex (AUD) reacts with free duplex giving triplex (UAUD) and free poly(A); moreover, ligand exchange between duplex and triplex occurs. A reaction mechanism is proposed and the reaction parameters are evaluated. For C(D)/C(P)> 0.8 poly(A)*poly(U) does not disproportionate at 25 degrees C and dye intercalation into AU to give AUD is the only observed process. Melting experiments as well show that coralyne induces the duplex disproportionation. Effects of temperature, ionic strength and ethanol content are investigated. One concludes that triplex formation requires coralyne be only partially intercalated into AUD. Under suitable concentration conditions, this feature favours the interaction of free AU with AUD to give the AUDAU intermediate which evolves into triplex UAUD and single-stranded poly(A). Duplex poly(A)*poly(A) undergoes aggregation as well, but only at much higher polymer concentrations compared to poly(A)*poly(U).