R. Prado-Gotor

Rational design of a CD4 mimic that inhibits HIV-1 entry and exposes cryptic neutralization epitopes

The conserved surfaces of the human immunodeficiency virus (HIV)-1 envelope involved in receptor binding represent potential targets for the development of entry inhibitors and neutralizing antibodies. Using structural information on a CD4-gp120-17b antibody complex, we have designed a 27-amino acid CD4 mimic, CD4M33, that presents optimal interactions with gp120 and binds to viral particles and diverse HIV-1 envelopes with CD4-like affinity. This mini-CD4 inhibits infection of both immortalized and primary cells by HIV-1, including primary patient isolates that are generally resistant to inhibition by soluble CD4. Furthermore, CD4M33 possesses functional properties of CD4, including the ability to unmask conserved neutralization epitopes of gp120 that are cryptic on the unbound glycoprotein. CD4M33 is a prototype of inhibitors of HIV-1 entry and, in complex with envelope proteins, a potential component of vaccine formulations, or a molecular target in phage display technology to develop broad-spectrum neutralizing antibodies.

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.

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.

Electron transfer reactions in micellar systems: Separation of the true (unimolecular) electron transfer rate constant in its components

Abstract The intramolecular electron transfer reaction within the binuclear complex [(en) 2 Co III (μ-2-pzCO 2 )Fe II (CN) 5 ] − has been studied in micellar (dodecylsulphate sodium salt (SDS) and hexadecyltrimethylammonium chloride (CTACl)) solutions. The true (unimolecular) electron transfer rate constant as well as the parameters controlling this rate constant, the reorganization free energy and the reaction free energy were obtained. This has permitted us to establish that, in spite of the similar behaviour observed for k et in both kinds of micellar solutions, in the case of SDS solutions the kinetics is controlled by both the driving force and the reorganization energy. In the case of CTACl, only the reorganization energy controls the k et variations.

Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research

The interactions of DNA, whether long, hundred base pair chains or short-chained oligonucleotides, with ligands play a key role in the field of structural biology. Its biological activity not only depends on the thermodynamic properties of DNA-ligand complexes, but can and often is conditioned by the formation kinetics of those complexes. On the other hand, gold nanoparticles have long been known to present excellent biocompatibility with biomolecules and are themselves remarkable for their structural, electronic, magnetic, optical and catalytic properties, radically different from those of their counterpart bulk materials, and which make them an important asset in multiple applications. Therefore, thermodynamic and kinetic studies of the interactions of DNA with nanoparticles acting as small ligands are key for a better understanding of those interactions to allow for their control and modulation and for the opening of new venues of research in nanomedicine, analytic and biologic fields. The interactions of gold nanoparticles with both DNA polymers and their smaller subunits; special focus is placed on those interactions taking place with nonfunctionalized gold nanoparticles are reviewed in the present work.

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.

On the equivalence of the pseudophase related models and the Brönsted approach in the interpretation of reactivity under restricted geometry conditions

The equivalence of the Pseudophase and related models, frequently used in the interpretation of kinetic data under restricted geometry conditions, and the well known Brönsteds equation, used in the interpretation of the reactivity in homogeneous media, has been proven in several cases. The generalisation in relation to other non-kinetic properties such as reaction free energy and redox potentials has also been considered.

ELECTRON TRANSFER REACTIONS IN MICELLAR SYSTEMS

The influence of micelles on electron transfer processes is reviewed. The micelles modify the rate of electron transfer reactions by producing changes in all the relevant parameters controlling this rate; that is, through modification of the reorganization free energy, the reaction free energy, the nuclear dynamics and the strength of the coupling between the donor and the acceptor. Applications of studies on electron transfer reactions in micellar systems in different fields are presented.

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.