Reversible DNA compaction induced by partial intercalation of 16-Ph-16 gemini surfactants: evidence of triple helix formation.

The interaction between calf thymus DNA and the gemini surfactants N,N'-[α,ω-phenylenebis(methylene)bis [N,N'-dimethyl-N-(1-hexadecyl)]-ammonium dibromide], p-16-Ph-16 (α = 1, ω = 3) and m-16-Ph-16 (α = 1, ω = 2), has been investigated via circular dichroism, fluorescence and UV-vis spectroscopy, zeta potential, dynamic light scattering, and AFM microscopy. Measurements were carried out in aqueous media at different molar ratios, R = (C16-Ph-16)/CDNA and C16-Ph-16 always below the critical micellar concentration (CMC) of the surfactant. Under these conditions, DNA undergoes two reversible conformational changes, compaction and decompaction, due to interaction with the surfactant molecules at low and high molar ratios, respectively. The extent of such conformational changes is correlated with both the degree of surfactant partial intercalation, and the size and charge of the surfactant aggregates formed, in each case. Comparison of the results shows that the para-form of the surfactant intercalates into the DNA to a major extent; therefore, the compaction/decompaction processes are more effective. Among these, the structure of the resulting 16-Ph-16/DNA decompacted complex is worthy of note. For the first time it can be demonstrated that the partial intercalation of the 16-Ph-16 gemini surfactants induces the formation of triplex DNA-like structures at a high R ratio.

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.