Fluorescence-labeled bis-benzamidines as fluorogenic DNA minor-groove binders: photophysics and binding dynamics.

In recent decades there has been great interest in the design of highly sensitive sequence-specific DNA binders. The eligibility of the binder depends on the magnitude of the fluorescence increase upon binding, related to its photophysics, and on its affinity and specificity, which is, in turn, determined by the dynamics of the binding process. Therefore, progress in the design of DNA binders requires both thorough photophysical studies and precise determination of the association and dissociation rate constants involved. We have studied two bis-benzamidine (BBA) derivatives labeled by linkers of various lengths with the dye Oregon Green (OG). These fluorogenic binders show a dramatic fluorescence enhancement upon binding to the minor groove of double-stranded (ds) DNA, as well as significant improvement in their sequence specificity versus the parent BBA, although with decreased affinity constants. Detailed photophysical analysis shows that static and dynamic quenching of the OG fluorescence by BBA through photoinduced electron transfer is suppressed upon insertion of BBA into the minor groove of DNA. Fluorescence correlation spectroscopy yields precise dynamic rate constants that prove that the association process of these fluorogenic binders to dsDNA is very similar to that of BBA alone and that their lower affinity is mainly a consequence of their weaker attachment to the minor groove and the resultant faster dissociation process. The conclusions of this study will allow us to go one step further in the design of new DNA binders with tunable fluorescence and binding properties.

Single-molecule chemical denaturation of riboswitches.

To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg(2+) ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods.

Role of electrostatic and hydrophobic forces in the interaction of ionic dyes with charged micelles.

The nature and strength of the interactions between a cationic fluorophore, Rhodamine 123 (R123), and surfactants of different head charge are investigated. Series of absorption and fluorescence emission spectra and of fluorescence decays are measured. R123 does not interact with the monomers of both nonionic and cationic surfactants but it presents affinity to their micelles. A partition equilibrium model was proposed and the corresponding equilibrium constants were obtained, as well as the photophysical properties of the dye bound to the micelles. In the case of the cationic surfactants, changes of the fluorescence properties were already observed below the critical micellar concentration (CMC) due to dynamic quenching caused by the free counterions. In the presence of anionic surfactants R123 shows a very different behaviour with dramatic spectral changes below the CMC. The observed variations are attributed to a first, strong interaction between R123 and the surfactant monomers, which yields ionic pairs of singular photophysical properties and dominates at low surfactant concentrations, followed by the association of R123 with the surfactant premicellar and micellar aggregates at higher surfactant concentrations near the CMC. This behaviour results from the competition between the strong electrostatic interactions of the cationic dye with the anionic surfactant head groups and the hydrophobic forces stabilizing the dye inside the micelles. The results of this work illustrate the complex physicochemical and photophysical behaviour of a charged dye in micellar systems, which resembles the expected situation in similar systems such as biological membranes.

Host-guest complexation studied by fluorescence correlation spectroscopy: adamantane-cyclodextrin inclusion.

The host-guest complexation between an Alexa 488 labelled adamantane derivative and beta-cyclodextrin is studied by Fluorescence Correlation Spectroscopy (FCS). A 1:1 complex stoichiometry and a high association equilibrium constant of K = 5.2 x 10(4) M(-1) are obtained in aqueous solution at 25 degrees C and pH = 6. The necessary experimental conditions are discussed. FCS proves to be an excellent method for the determination of stoichiometry and association equilibrium constant of this type of complexes, where both host and guest are nonfluorescent and which are therefore not easily amenable to standard fluorescence spectroscopic methods.

Host-assisted guest self-assembly: enhancement of the dimerization of pyronines Y and B by gamma-cyclodextrin.

Buckle up! The dimerization of small fluorescent guests is strongly enhanced in presence of a cyclodextrin host. The host cavity acts like a belt to assist the self-assembly of guests (see picture). Small variations in the guest structure have significant influence on the stability and geometry of the aggregates.The role of small variations in the structural properties of host and guest molecules on the stoichiometry and strength of supramolecular associations is analyzed. Earlier we found that a change in substituents from pyronine B to pyronine Y has a dramatic effect on both the stability and the dynamics of the association of these guests with beta-cyclodextrin as host. Now we study the association between these two pyronines and a cyclodextrin with a bigger cavity (gamma-cyclodextrin) using UV/Vis absorption and fluorescence spectroscopy. The absorption spectra of the pyronines show complex variations with cyclodextrin concentration indicating that pyronine dimerization is strongly enhanced inside the cavity of the cyclodextrin. A full model is proposed and the equilibrium constants of the involved processes and the absorption and emission spectra of the different species are estimated. The equilibrium constants of the formation of complexed dimers are much higher than those for free dimerization or for the inclusion of a single guest. The gamma-cyclodextrin host acts like a belt to assist the guest self-assembly. The differences in the stability of pyronine B and pyronine Y dimers are explained on the basis of their structure and geometry.

Exchange-dynamics of a neutral hydrophobic dye in micellar solutions studied by Fluorescence Correlation Spectroscopy.

The dynamics of the exchange of the moderately hydrophobic neutral dye Coumarine 152 between the aqueous phase and the phase formed by neutral Triton X-100 micelles is studied by Fluorescence Correlation Spectroscopy. The changes in the photophysical properties of the dye in presence of the micelles are discussed. The low quantum yield, the low saturation threshold and the necessary high energetic excitation of this dye requires a careful selection of the experimental conditions in order to obtain dynamic and diffusional properties with reasonable precision. It is shown that the contrast between the brightness of free and bound dye has a strong influence on the sensitivity of the FCS experiment. The entry rate constant of the dye to the micelles, k(+)=(0.8±0.3)×10(10) M(-1) s(-1), is very near to the diffusion controlled limit. The high association equilibrium constant of K=(129±3)×10(3) M(-1) is mainly determined by the low exit rate constant, k(-)=(0.6±0.2)×10(5) s(-1).