Single-Bond Association Kinetics Determined by Tethered Particle Motion: Concept and Simulations

Ultrasensitive Single-Molecule Biosensor by Periodic Modulation of Magnetic Particle Motion

Ultrasensitive detection of low-abundance biomarkers by modern single-molecule technologies is critical for better diagnosis of severe diseases, but inevitable nonspecific bindings often cause fluctuations in the single-molecule counting results. Here we present an approach to improve the specificity in a single-molecule immunoassay by translating molecular binding signals into periodic nanomotion of magnetic particles. The sandwiched immunoassay is modified by using a long linker to tether one antibody onto a gold-covered substrate and a magnetic particle with another antibody coated as the reporter. By actively oscillating the particles with alternating magnetic fields, we could reliably identify specific binding through intensity fluctuation in plasmonic images of single particles. As a proof of concept, we demonstrate the detection of IFN-γ at the femtomolar level by the digital counting of specifically bound molecules. This active strategy outperforms existing passive motion-based approaches in sensitivity and speed, paving the way for disease diagnosis with low-abundance biomarkers.

Optimizing Binding among Bimolecular Tethered Complexes

Tethered motion is ubiquitous in nature, offering controlled movement and spatial constraints to otherwise chaotic systems. The enhanced functionality and practical utility of tethers has been exploited in biotechnology, catalyzing the design of novel biosensors and molecular assembly techniques. While notable technological advances incorporating tethered motifs have been made, a theoretical gap persists within the paradigm, hindering a comprehensive understanding of tethered-based technologies. In this work, we focus on the characterization of the binding kinetics of two tethered molecules functionalized to a hard surface. Using a mean-field approximation, the binding time of such bimolecular system is determined analytically. Furthermore, estimates of the grafting site separation and polymer lengths which expedite binding are provided. These estimates, along with the analytical theories and frameworks established here, have the potential to improve efficacy in self-assembly methods in DNA nanotechnology and can be extended to more biologically specific endeavors including targeted drug-delivery and molecular sensing.

Magnetic-Responsive Surface-Enhanced Raman Scattering Platform with Tunable Hot Spot for Ultrasensitive Virus Nucleic Acid Detection

Surface-enhanced Raman scattering (SERS)-based biosensors are promising tools for virus nucleic acid detection. However, it remains challenging for SERS-based biosensors using a sandwiching strategy to detect long-chain nucleic acids such as nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because the extension of the coupling distance (CD) between the two tethered metallic nanostructures weakens electric field and SERS signals. Herein, we report a magnetic-responsive substrate consisting of heteoronanostructures that controls the CD for ultrasensitive and highly selective detection of the N gene of SARS-CoV-2. Significantly, our findings show that this platform reversibly shortens the CD and enhances SERS signals with a 10-fold increase in the detection limit from 1 fM to 100 aM, compared to those without magnetic modulation. The optical simulation that emulates the CD shortening process confirms the CD-dependent electric field strength and further supports the experimental results. Our study provides new insights into designing a stimuli-responsive SERS-based platform with tunable hot spots for long-chain nucleic acid detection.

Imaging the Heterogeneous Localization of a Single Molecule

Single-molecule localization allows determining the underlying biological and biochemical processes and promotes the development of super-resolution imaging techniques. Here, we present an optical technique of tracking the motion of a single nanoparticle linked to a substrate via a biomolecule tether to reveal the localization of single biomolecules and the transient states of single nanoparticle switching between specific binding pairs. The affinities, steric hindrance, and conformational variation of a single-molecule binding pair uncover the dynamic details and intrinsic mechanism of binding processes with high specificity and accuracy (a few nanometers). The application of tracking motions of single soft liposomes on different modified surfaces was further demonstrated, which revealed the characteristic behavior related to surface chemistry. Our results show that the trajectory of nanoscale liposomes loaded with small-drug molecules is linked to the compositional inhomogeneity, which provides a route for thorough comprehension of the fundamental biotechnological process.

Statistical physics and mesoscopic modeling to interpret tethered particle motion experiments

Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques provide raw data such as the tracked particle amplitude of movement, from which relevant information about DNA conformations or states must be recovered. Solving this inverse problem appeals to specific theoretical tools that have been designed in the two last decades, together with the data pre-processing procedures that ought to be implemented to avoid biases inherent to these experimental techniques. These statistical tools and models are reviewed in this paper.

Probing Mitotic CENP-E Kinesin with the Tethered Cargo Motion Assay and Laser Tweezers

Coiled-coil stalks of various kinesins differ significantly in predicted length and structure; this is an adaption that helps these motors carry out their specialized functions. However, little is known about the dynamic stalk configuration in moving motors. To gain insight into the conformational properties of the transporting motors, we developed a theoretical model to predict Brownian motion of a microbead tethered to the tail of a single, freely walking molecule. This approach, which we call the tethered cargo motion (TCM) assay, provides an accurate measure of the mechanical properties of motor-cargo tethering, verified using kinesin-1 conjugated to a microbead via DNA links in vitro. Applying the TCM assay to the mitotic kinesin CENP-E unexpectedly revealed that when walking along a microtubule track, this highly elongated molecule with a contour length of 230 nm formed a 20-nm-long tether. The stalk of a walking CENP-E could not be extended fully by application of sideways force with optical tweezers (up to 4 pN), implying that CENP-E carries its cargo in a compact configuration. Assisting force applied along the microtubule track accelerates CENP-E walking, but this increase does not depend on the presence of the CENP-E stalk. Our results suggest that the unusually large stalk of CENP-E has little role in regulating its function as a transporter. The adjustable stalk configuration may represent a regulatory mechanism for controlling the physical reach between kinetochore-bound CENP-E and spindle microtubules, or it may assist localizing various kinetochore regulators in the immediate vicinity of the kinetochore-embedded microtubule ends. The TCM assay and underlying theoretical framework will provide a general guide for determining the dynamic configurations of various molecular motors moving along their tracks, freely or under force.

Continuous biomarker monitoring by particle mobility sensing with single molecule resolution

Healthcare is in demand of technologies for real-time sensing in order to continuously guard the state of patients. Here we present biomarker-monitoring based on the sensing of particle mobility, a concept wherein particles are coupled to a substrate via a flexible molecular tether, with both the particles and substrate provided with affinity molecules for effectuating specific and reversible interactions. Single-molecular binding and unbinding events modulate the Brownian particle motion and the state changes are recorded using optical scattering microscopy. The technology is demonstrated with DNA and protein as model biomarkers, in buffer and in blood plasma, showing sensitivity to picomolar and nanomolar concentrations. The sensing principle is direct and self-contained, without consuming or producing any reactants. With its basis in reversible interactions and single-molecule resolution, we envisage that the presented technology will enable biosensors for continuous biomarker monitoring with high sensitivity, specificity, and accuracy.