Assembly and Characterization of a Slingshot DNA Nanostructure for the Analysis of Bivalent and Bispecific Analytes with Biosensors.

The characterization of novel therapeutic antibodies with multivalent or multispecific binding sites requires new measurement modalities for biosensors, to discriminate the engagement of antigens via one, two, or even more binding moieties. The presentation of antigens on a sensor surface in a well-controlled spatial arrangement is a prerequisite for the successful interpretation of binding kinetics measurements of multivalent analytes, but the adjustment of defined distances between immobilized ligands is difficult to achieve in state-of-the-art biosensor systems. Here, we introduce a simple DNA nanostructure resembling a slingshot, which can be configured with two identical or two different antigens (bivalent or bispecific), which are spaced at a defined distance. We characterize the slingshot structure with a chip-based biosensor using electrically switchable DNA nanolevers and demonstrate that bivalent and monovalent antibodies selectively interact with slingshots that have been functionalized with two identical or two different antigens, respectively. The dissociation kinetics are quantified in real-time measurements and we show that the slingshot structure enables a clear differentiation between affinity and avidity effects.

Suppression of Photoanodic Surface Oxidation of n-Type 6H-SiC Electrodes in Aqueous Electrolytes.

The photoelectrochemical characterization of silicon carbide (SiC) electrodes is important for enabling a wide range of potential applications for this semiconductor. However, photocorrosion of the SiC surface remains a key challenge, because this process considerably hinders the deployment of this material into functional devices. In this report, we use cyclic voltammetry to investigate the stability of n-type 6H-SiC photoelectrodes in buffered aqueous electrolytes. For measurements in pure Tris buffer, photogenerated holes accumulate at the interface under anodic polarization, resulting in the formation of a porous surface oxide layer. Two possibilities are presented to significantly enhance the stability of the SiC photoelectrodes. In the first approach, redox molecules are added to the buffer solution to kinetically facilitate hole transfer to these molecules, and in the second approach, water oxidation in the electrolyte is induced by depositing a cobalt phosphate catalyst onto the semiconductor surface. Both methods are found to effectively suppress photocorrosion of the SiC electrodes, as confirmed by atomic force microscopy and X-ray photoelectron spectroscopy measurements. The presented study provides straightforward routes to stabilize n-type SiC photoelectrodes in aqueous electrolytes, which is essential for a possible utilization of this material in the fields of photocatalysis and multimodal biosensing.

Quantitation of affinity, avidity, and binding kinetics of protein analytes with a dynamically switchable biosurface.

A label-free method for the analysis of interactions of proteins with surface-tethered ligands is introduced. Short DNA levers are electrically actuated on microelectrodes by ac potentials, and their switching dynamics are measured in real-time by fluorescence energy transfer. Binding of proteins to ligands attached to the top of the DNA levers is detected by time-resolved measurements of the levers' dynamic motion. We demonstrate the quantitation of binding kinetics (k(on), k(off) rate constants), dissociation constants (K(D) in the pM regime), and the influence of competitive binders (EC(50) values). Moreover, the "switchSENSE" method reveals avidity effects and allows discriminating between analytes with one or more binding sites. In a comparative study, interactions of six hexa-histidine-tagged proteins with tris-nitrilotriacetic acid (NTA(3)) ligands are quantitated. Their binding kinetics and affinities are found to vary over up to 2 orders of magnitude, evidencing that the proteins' individual chemical environments significantly influence the His(6)-NTA(3) interaction.

Protein analysis by time-resolved measurements with an electro-switchable DNA chip.

Measurements in stationary or mobile phases are fundamental principles in protein analysis. Although the immobilization of molecules on solid supports allows for the parallel analysis of interactions, properties like size or shape are usually inferred from the molecular mobility under the influence of external forces. However, as these principles are mutually exclusive, a comprehensive characterization of proteins usually involves a multi-step workflow. Here we show how these measurement modalities can be reconciled by tethering proteins to a surface via dynamically actuated nanolevers. Short DNA strands, which are switched by alternating electric fields, are employed as capture probes to bind target proteins. By swaying the proteins over nanometre amplitudes and comparing their motional dynamics to a theoretical model, the protein diameter can be quantified with Angström accuracy. Alterations in the tertiary protein structure (folding) and conformational changes are readily detected, and even post-translational modifications are revealed by time-resolved molecular dynamics measurements.