E. Grueso

Thermodynamic and structural study of phenanthroline derivative ruthenium complex/DNA interactions: probing partial intercalation and binding properties.

The binding of [Ru(PDTA-H(2))(phen)]Cl (PDTA = propylene-1,2-diaminetetra-acetic acid; phen = 1,10 phenanthroline) with ctDNA (=calf thymus DNA) has been investigated through intrinsic and induced circular dichroism, UV-visible absorption and fluorescence spectroscopies, steady-state fluorescence, thermal denaturation technique, viscosity and electrochemical measurements. The latter indicate that the cathodic and anodic peak potentials of the ruthenium complex shift to more positive values on increasing the DNA concentration, this behavior being a direct consequence of the interaction of both the reduced and oxidized form with DNA binding. From spectrophotometric titration experiments, the equilibrium binding constant and the number of monomer units of the polymer involved in the binding of one ruthenium molecule (site size) have been quantified. The intrinsic circular dichroism (CD) spectra show an unwinding and a conformational change of the DNA helix upon interaction of the ruthenium complex. Quenching process, thermal denaturation experiments and induced circular dichroism (ICD) are consistent with a partial intercalative binding mode.

Compaction and decompaction of DNA induced by the cationic surfactant CTAB.

A multifaceted study on the interaction of the cationic surfactant CTAB with calf thymus DNA was carried out by using different techniques. The measurements were done at different molar ratios X = [CTAB]/[DNA]. Results show the conformational change that DNA suffers due to the interaction with surfactant molecules at low molar ratios: the condensation of the polynucleotide, from an extended coil state to a globular state. The effect observed at the higher molar ratios is worth noting: the decondensation of DNA, that is, the transition from a compact state to a more extended conformation. Experimental data obtained confirm that this latter state is not exactly the same as that found in the absence of the surfactant. Attractive interactions between different parts of the molecule by ion correlation effects are the driving force to produce both the compaction and decompaction events. Results also show the importance of choosing both a proper system for the study and the most seeming measuring technique to use. The study demonstrates that, in some cases, the use of several techniques is desirable in obtaining reliable and accurate results.

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.

Nonfunctionalized Gold Nanoparticles: Synthetic Routes and Synthesis Condition Dependence

Since Faraday first described gold sol synthesis, synthetic routes to nanoparticles, as well as their applications, have experienced a huge growth. Variations in synthesis conditions such as pH, temperature, reduction, and the stabilizing agent used will determine the morphology, size, monodispersity, and stability of nanoparticles obtained, allowing for modulation of their physical and chemical properties. Although many studies have been made about the synthesis and characterization of individual nanosystems of interest, to our knowledge the common, general traits that all those synthesis share have not been previously compiled. In this review, we aim to offer a global vision of some of the most relevant synthetic procedures reported up to date, with a special focus on nonfunctionalized gold nanoparticle synthetic routes in aqueous media, and to display a broad overview of the influence that synthesis conditions have on the shape, stability, and reactivity of nanoparticle systems.

Kinetic Study of the Cetyltrimethylammonium/DNA Interaction

A kinetic study of the interaction of the surfactant cetyltrimethylammonium (CTA(+)) with DNA was carried out in water and in salt (NaCl) solutions. The results can be explained in terms of a reaction mechanism involving two consecutive reversible steps. The first step corresponds to the union/separation of the surfactant with/from the DNA. The second step corresponds to a conformational change of the surfactant/DNA complex. The equilibrium constant, calculated from the forward and reverse rate constants of these steps, agrees with the results of a previous thermodynamic study.

DNA conformational changes induced by cationic gemini surfactants: the key to switching DNA compact structures into elongated forms

The DNA conformational changes induced by different members of the N,N′-bis(dimethyldodecyl)-α-ω-alkanediammonium dibromide series (m-s-m, m = 12, s = 3 and 6) and the analogous series of hexadecyl gemini surfactants (m = 16, s = 3 and 6) were investigated in aqueous media by means of circular dichroism (CD), zeta potential, dynamic light scattering (DLS), viscometry, and atomic force microscopy (AFM) methods. The measurements were carried out by varying the gemini surfactant–DNA molar ratio, R = Cm-s-m/CDNA. For the conditions investigated two significantly different conformational changes were observed, the second of them being worth noting. At low molar ratios, all methods concurred by showing that gemini surfactants were able to form ordered aggregates which precedes DNA compaction. The second effect observed, at high molar ratios, corresponds to the transition from the compact state to a new more extended conformation. The degree of decompaction and the morphologies of the visualized structures are different not only depending on the surfactant tails length, but also on the spacers length. The results obtained for the 16-3-16/DNA and 16-6-16/DNA systems point out that the compaction/decompaction processes are somewhat different to those previously visualized for the analogous monoquaternary chain surfactant CTAB.

Improving the understanding of DNA–propanediyl-1,3-bis(dodecyldimethylammonium) dibromide interaction using thermodynamic, structural and kinetic approaches

A kinetic, thermodynamic and structural study of the interaction of the gemini surfactant propanediyl-1,3-bis(dimethyldodecylammonium dibromide) (12-3-12.2Br) with calf thymus DNA was carried out at several ionic strengths (NaCl) in aqueous solutions. A new 12-3-12(2+)-selective membrane was prepared in order to gain insight into the factors that control the binding of 12-3-12.2Br to DNA. We used ethidium bromide (EB) as a fluorescence probe to follow the kinetics of the interaction by using the stopped-flow fluorescence technique. The results can be explained in terms of a reaction mechanism involving two consecutive reversible (fast and slow) steps. The fast step was attributed to the union/separation of the surfactant with/from the DNA polynucleotide. Changes in the kinetic constants in the forward and backward directions were discussed in terms of the Brönsted-Pitzer equation and of the increase in hydrophobic interactions of the surfactant tails as a consequence of salting-out effects, respectively. The slow step corresponds to a conformational change of the surfactant-DNA complex to a more compacted form. The equilibrium constant, calculated from the forward and reverse rate constants of these steps, agrees with the results obtained from potentiometric titration using a 12-3-12-(2+) selective electrode.

Noncovalent interactions of tiopronin-protected gold nanoparticles with DNA: two methods to quantify free energy of binding.

The binding of gold nanoparticles capped with N-(2-mercaptopropionyl)glycine (Au@tiopronin) with double-stranded DNA has been investigated and quantified in terms of free energies by using two different approaches. The first approach follows the DNA conformational changes induced by gold nanoparticles using the CD technique. The second methodology consists in the use of pyrene-1-carboxaldehyde as a fluorescent probe. This second procedure implies the determination of the “true” free energy of binding of the probe with DNA, after corrections through solubility measurements. Working at different salt concentrations, the nonelectrostatic and electrostatic components of the binding free energy have been separated. The results obtained revealed that the binding is of nonelectrostatic character, fundamentally. The procedure used in this work could be extended to quantify the binding affinity of other AuNPs/DNA systems.

Electrochemiluminescent (ECL) [Ru(bpy)3]2+/PAMAM dendrimer reactions: coreactant effect and 5-fluorouracil/dendrimer complex formation

AbstractElectrogenerated chemiluminescence (ECL) reactions between tris(2,2′-bipyridine)ruthenium(II) and PAMAM dendrimers of the full (G1.0) and half (G1.5) generations were carried out in an aqueous medium at pH 6.1 and 10.0. In the absence of 5-fluoro-1H,3H-pyrimidine-2,4-dione (5-fluorouracil, 5-Fu) (coreactant effect study), the ECL efficiency trends as a function of [G1.0] and [G1.5] at pH 6.1 and 10.0 revealed that PAMAM dendrimers are about 100 (G1.5, pH 6.1), 60 (G1.5, pH 10.0), 26 (G1.0, pH 10.0) and 13 (G1.0, pH 6.1) times more efficient as ECL coreactants than oxalate anion is. Moreover, ECL reactions were done in the presence of several solutions of 5-Fu at a fixed concentration of the G1.0 and G1.5 dendrimers at pH 6.1 and 10.0 (binding study). The ECL efficiency trends as a function of [5-Fu] highlighted a dendrimer/5-Fu binding. Therefore, one of the most remarkable and novel findings of this work is the potential of PAMAM dendrimers to be used as both sensors and biosensors in an aqueous medium in the presence of a suitable sensitizer. Redox potentials of the [Ru(bpy)3]3+/2+ couple were also determined in the absence and presence of 5-Fu at both pHs. In the absence of 5-Fu the positive or negative shift of redox potentials showed the influence of the repulsive or attractive electrostatic long-range and short-range interactions between the charged dendrimer surface and the oxidized and reduced forms of the couple. In the presence of 5-Fu the trends of redox potentials highlighted the existence of a charged dendrimer/5-Fu species. Graphical AbstractECL emission for the [Ru(bpy)3]2+/ G1.0 dendrimer reaction in the presence of the 5-Fu at pH 6.1

Ethanol effect on gold nanoparticle aggregation state and its implication in the interaction mechanism with DNA

The equilibria and kinetics aspects of the binding of small gold nanoparticles, AuNPs, stabilized with tiopronin to DNA in B and C conformation (B-DNA and C-DNA), has been investigated in ethanol/water mixtures using different techniques. Two modes of binding are displayed: groove binding and partial intercalation, depending on the ethanol content, [EtOH], and the molar ratio, R = CAuNPs/CDNA. Two reaction mechanisms are proposed for AuNPs/DNA interaction in each polymer conformation, and the reaction parameters are evaluated. For lower ethanol levels, ([EtOH] up to 30%), when DNA is in the B form, the simplest mechanism according to the kinetic and thermodynamic results proved to be a three-step series mechanism reaction scheme which evolves in the formation of the groove complex. In this context, solvent hydration as well as the solvent effective viscosity are the main factors that influence kinetics. In contrast, for high ethanol levels, when DNA is in a C-like conformation, the mechanism is more complex involving three parallel reactions, in which AuNPs self-aggregation plays a key role in the switch from partial intercalation to groove binding. On the whole, it is evident that AuNPs aggregation and the DNA conformation are two key factors that must be taken into account in order to control the mechanism of AuNPs/DNA interaction.