Real-time kinetic, affinity and conformational insights using dynamic DNA nanolevers.
Experience next generation biosensing, now available at our Strasbourg facilities.
The switchSENSE® biosensor technology enables real-time monitoring of molecular interactions between an immobilized ligand and an analyte in solution.
Using DNA nanolevers to capture ligands on the chip surface, switchSENSE® provides unique access to interaction kinetics, specificity, conformational changes, and ternary complex formation — all in a single versatile platform applicable to proteins, peptides and small molecules.
Key Capabilities
Affinity & Kinetics
- Measure KD, kon, koff in real time using static mode with fluorescence proximity sensing.
- Capture fast or slow interactions with high precision.
Specificity
- Dual-fluorophore detection allows simultaneous assessment of an analyte against two different ligands immobilized on the same surface.
- Reduce false positives and enhance confidence in binding profiles.
Ternary Complexes & Avidity
- Study PROTACs, molecular glues, or protein–protein interaction modulators using Y-shaped DNA nanostructures.
- FRET-based detection monitors interactions between two ligands in the presence of an analyte.
Conformational Dynamics
- Using dynamic mode, DNA nanolevers oscillate, providing direct insight into molecular conformational changes: expansion (slower motion) or compaction (faster motion).
Why switchSENSE®?
- Highly versatile: applicable to proteins and peptides.
- Accelerates drug discovery: from affinity and kinetics to complex formation and conformational analysis.
- Exclusive access: test cutting-edge biosensing now in Strasbourg.
Visualizing switchSENSE® in action
Among the different chips offered by Bruker, the Y-structure proximity assay (Figure 1.) is particularly well suited for the characterization of PROTAC molecules. In this setup, the protein of interest and the E3 ubiquitin ligase are attached to the distal arm lengths. Green and red fluorophores are attached to the distal ends of the swivel arms to detect binary binding via fluorescence quenching, while ternary binding is detected by a FRET signal when the arms are closed.
Figure 1.
The Y-structure has been used to efficiently assess PROTAC-mediated ternary complex formation. Seven PROTAC molecules were evaluated (Figure 2.). The Y-shaped structure was functionalized with the target protein BRD4-BD1 on the green-dye arm and the E3 ligase CRBNmidi on the red-dye arm. BRD4-BD2 was also tested as a negative control for ternary complex formation. Fluorescence was excited in the green channel, while emissions from both channels were recorded simultaneously. Upon PROTAC injection, red emission was observed via green-to-red FRET as the Y-structure closed, indicating bridging of the target protein (BRD4) and ligase by the PROTAC.
Upon PROTAC dissociation, the arms returned to the open state, and fluorescence in both channels recovered to baseline. Binary binding of the PROTACs to BRD4-BD1 was additionally monitored using fluorescence proximity sensing (FPS).
Figure 2.
Kinetic characterization of binary and ternary complexes has been completed for seven PROTACs targeting CRBN and BRD4. In Figure 2., the top panel shows the FRET signal resulting from ternary complex formation with CRBNmidi and the target protein BRD4-BD1. In this assay, all PROTACs form ternary complexes with BRD4-BD1. The middle panel confirms the absence of ternary complex with the counter target BRD4-BD2 and bottom panel shows the binary binding to BRD4-BD1. PROTACs 1, 2, and 3 display highly similar behavior, forming tight ternary complexes with BRD4-BD1 and CRBNmidi, with dissociation constants in the high picomolar range. These compounds also exhibit strong and comparable binary binding to BRD4-BD1. For more details on the impact of the PROTAC molecules on the kon and koff parameters, please refer to our application note.
Discover how switchSENSE® can provide valuable insight into your binding characterization. Contact our experts.
