Multianalytical Study of the Binding between a Small Chiral Molecule and a DNA Aptamer: Evidence for Asymmetric Steric Effect upon 3'- versus 5'-End Sequence Modification.

Nucleic acid aptamers are involved in a broad field of applications ranging from therapeutics to analytics. Deciphering the binding mechanisms between aptamers and small ligands is therefore crucial to improve and optimize existing applications and to develop new ones. Particularly interesting is the enantiospecific binding mechanism involving small molecules with nonprestructured aptamers. One archetypal example is the chiral binding between l-tyrosinamide and its 49-mer aptamer for which neither structural nor mechanistic information is available. In the present work, we have taken advantage of a multiple analytical characterization strategy (i.e., using electroanalytical techniques such as kinetic rotating droplet electrochemistry, fluorescence polarization, isothermal titration calorimetry, and quartz crystal microbalance) for interpreting the nature of binding process. Screening of the binding thermodynamics and kinetics with a wide range of aptamer sequences revealed the lack of symmetry between the two ends of the 23-mer minimal binding sequence, showing an unprecedented influence of the 5' aptamer modification on the bimolecular binding rate constant kon and no significant effect on the dissociation rate constant koff. The results we have obtained lead us to conclude that the enantiospecific binding reaction occurs through an induced-fit mechanism, wherein the ligand promotes a primary nucleation binding step near the 5'-end of the aptamer followed by a directional folding of the aptamer around its target from 5'-end to 3'-end. Functionalization of the 5'-end position by a chemical label, a polydA tail, a protein, or a surface influences the kinetic/thermodynamic constants up to 2 orders of magnitude in the extreme case of a surface immobilized aptamer, while significantly weaker effect is observed for a 3'-end modification. The reason is that steric hindrance must be overcome to nucleate the binding complex in the presence of a modification near the nucleation site.

Sensor Based on Aptamer Folding to Detect Low-Molecular Weight Analytes.

Aptamers have emerged as promising biorecognition elements in the development of biosensors. The present work focuses on the application of quartz crystal microbalance with dissipation monitoring (QCM-D) for the enantioselective detection of a low molecular weight target molecule (less than 200 Da) by aptamer-based sensors. While QCM-D is a powerful technique for label-free, real-time characterization and quantification of molecular interactions at interfaces, the detection of small molecules interacting with immobilized receptors still remains a challenge. In the present study, we take advantage of the aptamer conformational changes upon the target binding that induces displacement of water acoustically coupled to the sensing layer. As a consequence, this phenomenon leads to a significant enhancement of the detection signal. The methodology is exemplified with the enantioselective recognition of a low molecular weight model compound, L-tyrosinamide (L-Tym). QCM-D monitoring of L-Tym interaction with the aptamer monolayer leads to an appreciable signal that can be further exploited for analytical purposes or thermodynamics studies. Furthermore, in situ combination of QCM-D with spectroscopic ellipsometry unambiguously demonstrates that the conformational change induces a nanometric decrease of the aptamer monolayer thickness. Since QCM-D is sensitive to the whole mass of the sensing layer including water that is acoustically coupled, a decrease in thickness of the highly hydrated aptamer layer induces a sizable release of water that can be easily detected by QCM-D.

Redox-driven host-guest interactions allow the controlled release of captured cells on RGD-functionalized surfaces.

A quartz crystal microbalance technique with dissipation monitoring and a complementary optical microscopy technique were used for monitoring the capture and release of specific cells on a surface displaying a bifunctional molecular device, composed of a molecular scaffold endowed with the cell recognition property of an RGD ligand and a ß-CD/Fc redox-switchable system.

Comparison of the density of proteins and peptides grafted on silane layers and polyelectrolyte multilayers.

Immobilized proteins or peptides are of critical importance for applications such as biosensing or cell culture. We analyze the structure of layers of a large variety of proteins and peptides, grafted on silicon substrates by different routes differing in the nature of the intermediate layer linking the biomolecules to the substrate, either a silane monolayer, or a polyelectrolyte multilayer made from synthetic or natural polymers. The structural analysis is essentially performed by X-ray reflectometry, which proves to be an efficient methodology not requiring the use of tagged biomolecules, capable of evaluating consistently the amount of grafted biomolecules per surface area with estimated precisions ranging from 10 to 20%. The study provides a quantitative basis for selecting one among a series of well-proofed and sturdy grafting methodologies and underlines the potential of XRR for assessing the amount of grafted biomacromolecules without requiring the expensive tagging of molecules. Our results also show that, for the coupling route resting on synthetic polyelectrolytes, the grafting density is significantly lower than for direct coupling over a silane layer. In contrast, when performed over a cushion based on polysaccharides, the grafting density is well above the values found for a dense layer grafted on a silane monolayer, indicating partial penetration and swelling of the polysaccharide cushion.

One-step vs stepwise immobilization of 1-D coordination-based Rh-Rh molecular wires on gold surfaces.

Reaction of dimeric [Rh(II)(2)(phen)(2)(µ-OAc)(2)(MeCN)(2)](BF(4))(2) (phen =1,10-phenanthroline) with pyrazine (pz) in a 1:2 ratio leads to the new 1-D metal-metal-bonded coordination oligomer {[Rh(II)(2)(phen)(2)(µ-OAc)(2)(pz)](BF(4))(2)}(n) (Rh-Rhpz)(n) (1), where each Rh atom of the dimeric unit (Rh-Rh) is coordinated in the equatorial plane to a nitrogen atom of a rigid and linear bifunctionalized organic linker (pz). Single X-ray diffraction analysis reveals the 1-D straight oligomeric chain structure (molecular wire, MW) consists of alternating (Rh-Rh) units and pz linking ligands with free BF(4)(-) as counteranions, and each metal center has a slightly distorted octahedral arrangement. The presence of accessible labile MeCN groups on both ends of these MWs ("free ends") enables functionalization of a 4-mercaptopyridine-gold coordinating platform (Au/MP) to form in one step a layer of coordination oligomer (Au/MP(Rh-Rhpz)(n); n ≈ 50). Furthermore (Rh-Rhpz)(n) (n = 1-6) MWs were grafted to Au/MP surfaces by a conventional step-by-step assembly construction involving coordination reactions between the Rh dimer ([Rh(2)(phen)(2)(µ-OAc)(2)(MeCN)(2)](BF(4))(2) (2)) and pz. A detailed physicochemical study (UV-vis, RAIR, QCM-D, ellipsometry, contact angle measurements, as well as impedance spectroscopy and cyclic voltammetry) has been made during both assembly methods to characterize the resulting surface-anchored coordination molecular wire (CMW) layers (Au/MP(Rh-Rhpz)(n)). The results indicate that the immobilized molecular assemblies (MAs) were successfully fabricated using both methods of assembly. The efficiency of the two methods is discussed.

Tethered bilayer lipid membranes on mixed self-assembled monolayers of a novel anchoring thiol: impact of the anchoring thiol density on bilayer formation.

Tethered bilayer lipid membranes (tBLMs) are designed on mixed self-assembled monolayers (SAMs) of a novel synthetic anchoring thiol, 2,3-di-o-palmitoylglycerol-1-tetraethylene glycol mercaptopropanoic acid ester (TEG-DP), and a new short dilution thiol molecule, tetraethylene glycol mercaptopropanoic acid ester (TEG). tBLM formation was accomplished by self-directed fusion of small unilamellar vesicles of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. The influence of the dilution of the anchoring thiol molecule in the SAM on the vesicle fusion process and on the properties of the resulting tBLMs is studied. It is observed by quartz crystal microbalance that vesicle fusion is a one-step process for a pure TEG-DP SAM as well as for mixed SAMs containing a high concentration of the anchoring thiol. However, upon dilution of the anchoring thiol to moderate concentrations, this process is decelerated and possibly follows a pathway different from that observed on a pure TEG-DP SAM. Electrochemical impedance spectroscopy is used to qualitatively correlate the composition of the SAM to the electrical properties of the tBLM. In this paper we also delineate the necessity of a critical concentration of this anchoring TEG-DP thiol as a requisite for inducing the fusion of vesicles to form a tBLM.

Controlled density patterning of tolylterpyridine-tagged oligonucleotides.

An efficient surface anchoring strategy of tolylterpyridine-tagged DNA single strands (ssDNA-ttpy) synthesized on gold electrodes is reported. The method is based on exchange reactions between Fe(II)bis-terpyridine complexed SAMs and ssDNA-ttpy, and allows efficient hybrydization of the cDNA strands. Moreover, by using low-current focused ion beam lithography, micropatterned arrays are obtained, homogeneously covered with ssDNA-ttpy. The surface adsorption kinetics of ssDNA-ttpy, as well as its hybridization efficiency, was monitored by in situ quartz crystal microbalance with dissipation monitoring (QCM-D) technique. The effective confinement of the ssDNA-ttpy at the micrometer level has been monitored by time of flight secondary ion mass spectrometry (ToF-SIMS) and ellipsometric surface imaging experiments, providing laterally resolved chemical and topographic mapping.

The flexible motif V of Epstein-Barr virus deoxyuridine 5'-triphosphate pyrophosphatase is essential for catalysis.

Deoxyuridine 5'-triphosphate pyrophosphatases (dUTPases) are ubiquitous enzymes essential for hydrolysis of dUTP, thus preventing its incorporation into DNA. Although Epstein-Barr virus (EBV) dUTPase is monomeric, it has a high degree of similarity with the more frequent trimeric form of the enzyme. In both cases, the active site is composed of five conserved sequence motifs. Structural and functional studies of mutants based on the structure of EBV dUTPase gave new insight into the mechanism of the enzyme. A first mutant allowed us to exclude a role in enzymatic activity for the disulfide bridge involving the beginning of the disordered C terminus. Sequence alignments revealed two groups of dUTPases, based on the position in sequence of a conserved aspartic acid residue close to the active site. Single mutants of this residue in EBV dUTPase showed a highly impaired catalytic activity, which could be partially restored by a second mutation, making EBV dUTPase more similar to the second group of enzymes. Deletion of the flexible C-terminal tail carrying motif V resulted in a protein completely devoid of enzymatic activity, crystallizing with unhydrolyzed Mg(2+)-dUTP complex in the active site. Point mutations inside motif V highlighted the essential role of lid residue Phe(273). Magnesium appears to play a role mainly in substrate binding, since in absence of Mg(2+), the K(m) of the enzyme is reduced, whereas the k(cat) is less affected.

Template-assembled synthetic G-quadruplex (TASQ): a useful system for investigating the interactions of ligands with constrained quadruplex topologies.

A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a pi-stacking binding mode showed a higher binding affinity for intermolecular-like G-quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G-quadruplex DNA over the duplex DNA. A numerical parameter, termed the G-quadruplex binding mode index (G4-BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G-quadruplex 1 against intramolecular G-quadruplex 2. The G-quadruplex binding mode index (G4-BMI) of a ligand is defined as follows: G4-BMI=K(D)(intra)/K(D)(inter), where K(D)(intra) is the dissociation constant for intramolecular G-quadruplex 2 and K(D)(inter) is the dissociation constant for intermolecular G-quadruplex 1. In summary, the present work has demonstrated that the use of parallel-constrained quadruplex topology provides more precise information about the binding modes of ligands.

Electrochemically controlled adsorption of Fc-functionalized polymers on beta-CD-modified self-assembled monolayers.

This work presents an in situ study of the adsorption/desorption behavior of ferrocene(Fc)-functionalized linear polymers on a gold surface covered with beta-cyclodextrin(beta-CD)-modified self-assembled monolayers (SAMs). The characterization of binary SAMs obtained with HS-(CH(2))(11)-EG(6)-N(3) and HS-(CH(2))(11)-EG(4)-OH (EG, ethylene glycol) was performed using a quartz crystal microbalance with dissipation monitoring (QCM-D), cyclic voltammetry, and contact angle measurements. The functionalization of SAMs with beta-CD was made via the "click" reaction between the beta-CD monoalkyne derivative and azide groups exhibited by SAMs. The formation of the host-guest complex between SAM-beta-CD and Fc-derivatized polymers (chitosan (CHI) and poly(allylamine hydrochloride) (PAH)) was studied by QCM-D. The viscoelastic model of Voinova was used to fit QCM-D curves recorded during the adsorption and electrochemically controlled desorption of CHI-Fc and PAH-Fc on SAM-beta-CD. Using QCM-D coupled to cyclic voltammetry, we demonstrated that CHI-Fc and PAH-Fc can be successfully deposited on a SAM-beta-CD-coated gold surface forming a stable multivalent inclusion complex between Fc moieties of polymer and beta-CD cavities of SAM. We also showed that all specifically attached polymer chains can be detached from the SAM-beta-CD-coated gold surface by applying an electric field.

Cell adhesion through clustered ligand on fluid supported lipid bilayers.

The quartz crystal microbalance technique with dissipation monitoring and the complementary optical microscopy technique were used for monitoring cell adhesion on an RGD-functionalized supported lipid bilayer. A critical interligand RGD spacing of nearly 80 nm was estimated for cell adhesion when an RGD spacing of 10 nm was necessary to observe flattened cells on a fluid surface.

Multilayer films based on host-guest interactions between biocompatible polymers.

Multilayer films are formed using host-guest interaction between two derivatized chitosans, one, with beta-cyclodextrin cavities and the other with adamantyl moieties.

Layer-by-layer self-assembled multilayers of redox polyelectrolytes and gold nanoparticles.

Construction and characterization of structural and charge transport properties of electrostatically LbL self-assembled multilayers of gold nanoparticles and a viologen-based redox-active polyelectrolyte is reported.

On the mucoadhesive properties of chitosan-coated polycaprolactone nanoparticles loaded with curcumin using quartz crystal microbalance with dissipation monitoring.

Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) was used to investigate the mucoadhesive properties of nanoparticles decorated with low, medium and high molar mass chitosan (CS). Uncoated and chitosan-coated polycaprolactone (PCL) nanoparticles loaded with curcumin were prepared by nanoprecipitation method and characterized in terms of size, surface charge and drug content. The interactions between nanoparticles and mucin layer were monitored after the treatment of SAM-functionalized gold-coated quartz crystals with bovine submaxillary gland mucin (BSM). The results show that all investigated chitosan-coated nanoparticles adsorb onto the BSM layer, and the mass uptake was found to be independent of the chitosan molar mass. Uncoated nanoparticles showed, however, no affinity with BSM layer, confirming that the adsorption of colloidal systems occurs due to their decoration with chitosan. The adhesion is mainly attributed to electrostatic interactions between protonated amino groups of mucoadhesive chitosan and negatively charged groups of mucin. The results suggest that chitosan-coated nanoparticles are promising carriers for hydrophobic drugs delivery in the buccal mucosa.

A quartz crystal microbalance method to study the terminal functionalization of glycosaminoglycans.

We demonstrate the quartz crystal microbalance as a novel method to quantify the reaction yields and stability of the terminal conjugation of chemically complex molecules. Oxime ligation is identified as a facile, broadly applicable method for the reducing-end conjugation of glycosaminoglycans that overcomes the limited stability and yield of popular hydrazone ligation.

Oligosaccharide biosensor for direct monitoring of enzymatic activities using QCM-D.

Enzymatic modification of saccharidic biomass is a subject of intensive research with potential applications in plant or human health, design of biomaterials and biofuel production. Bioengineering and metagenomics provide access to libraries of glycoside hydrolases but the biochemical characterization of these enzymes remains challenging, requiring fastidious colorimetric tests in discontinuous assays. Here, we describe a highly sensitive carbohydrate biosensor for the detection and characterization of glycoside hydrolases. Immobilization of oligosaccharides was achieved using copper-catalyzed azide-alkyne cycloaddition of maltoheptaose-modified probes onto self-assembled monolayers bearing azide reactive groups. This biosensor allowed detection of glycoside hydrolase activities at the picomolar level using quartz-crystal microbalance with dissipation monitoring (QCM-D). To our knowledge, this protocol provides the best performance to date for the detection of glycoside hydrolase activities. For each enzyme tested, we could determine the kinetic constant from the QCM-D data, and derive conclusions that correlated well with those of standard colorimetric tests. This opens the way to a new generation of rapid and direct tests characterizing functionally carbohydrate-active enzymes.

Characterization of a modified gold platform for the development of a label-free anti-thrombin aptasensor.

This work reports the characterization of a modified gold surface as a platform for the development of a label free aptasensor for thrombin detection. The biorecognition platform was obtained by the self-assembly of 4-mercaptobenzoic acid onto a gold surface, covalent attachment of streptavidin and further immobilization of the biotinylated anti-thrombin aptamer. The biosensing platform was characterized by cyclic voltammetry, electrochemical impedance spectroscopy, surface plasmon resonance (SPR) and quartz crystal microbalance with dissipation monitoring. The biorecognition event aptamer-thrombin was detected from changes in the SPR angle produced as a consequence of the molecular interaction between the aptasensor and the target protein. The biosensing platform demonstrated to be highly selective for human thrombin even in the presence of large excess of bovine thrombin, bovine serum albumin, cytochrome C, lysozyme and myoglobin. The relationship between the changes in the SPR angle and thrombin concentration was linear up to 0.19 µmol L(-1) (R(2)=0.992) while the detection limit was of 12.0 nmol L(-1) (240 fmol in the sample). This new sensing approach represents an interesting and promising alternative for the SPR-based quantification of thrombin.

Amphipol mediated surface immobilization of FhuA: a platform for label-free detection of the bacteriophage protein pb5.

Biotinylated amphipol was used to entrap FhuA (an E. coli outer membrane protein) and immobilize the FhuA-amphipol complex on streptavidin surfaces. Using this assembly, we have successfully devised surface-based assays for studying the recognition of FhuA by pb5 (a bacteriophage T5 protein) and determination of the affinity constant.