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April 17, 2025

How Depixus made magnetic force spectroscopy scalable and accessible in a user-friendly laboratory instrument

Magnetic Force Spectroscopy (MFS) is an analytical technique that directly probes the forces involved in individual biomolecular interactions. By taking this powerful approach and scaling it up to thousands of molecules in parallel, Depixus MAGNA One™ opens up a new world of insights into the intricate dynamics of biomolecular interactions that drive biological processes in health and disease.

The history and applications of magnetic force spectroscopy and magnetic tweezers

First developed more than 30 years ago, magnetic force spectroscopy (MFS) is a technique used to study the properties and interactions of biomolecules.​1,2

MFS apparatus is often referred to as magnetic tweezers. Molecules, such as DNA or RNA, are tethered to a flow cell surface at one end and attached at the other to paramagnetic beads, which are manipulated by a controllable external magnetic field. A camera tracks the movements of these beads, enabling precise measurement of the forces applied and the molecular response.

Magnetic tweezers are highly versatile and are compatible with various experimental setups. Their applications span numerous fields in biophysics and biology,3 providing unprecedented insights such as:

  • Macromolecular Mechanics: Investigating the mechanical properties of DNA,​2,4​ RNA,​5​ and double-stranded RNA.​6
  • Enzymatic Activities: Studying the actions and properties of DNA and RNA binding enzymes. For example, research by Depixus’ academic founders Vincent Croquette and David Bensimon and their teams has revealed critical insights into the dynamics and actions of helicases, polymerases, and topoisomerases – key players in gene regulation and replication.​7-10​
  • Protein Dynamics: Exploring protein folding, unfolding,​11​ and protein-protein interactions.​12
  • Cellular Mechanics: Examining the viscoelastic properties of the cytoplasm and the mechanical properties of living cells.​13,14

Limitations of conventional MFS methods

Despite its power and versatility, the widespread adoption of magnetic force spectroscopy has been hindered by its technical complexity and limitations in its scalability.

While the first use of a parallelized magnetic tweezer apparatus reported tracking of up to 34 beads as long ago as in 2008,​15 advances in throughput have been limited by camera and optical system capabilities, and bead tracking technologies.

Many magnetic tweezer systems rely on interferometric techniques for the detection of bead position. This typically requires several thousands of camera pixels to track the position of a single bead with high accuracy, limiting the number of beads that can be tracked in parallel. For example, the tracking system in the recently developed stereo dark-field interferometry magnetic force spectroscopy apparatus uses approximately 64×64 pixels per bead. 16

Throughput is also limited by the random distribution of molecules and their associated beads on the flow cell surface. If two beads are too close to each other they will interfere with each other’s movement and not provide analyzable data, while large gaps between beads create wasted space.

Recent advances have partially addressed the throughput of magnetic tweezers, with the ability to track over a hundred or a few thousand beads​ 16-18 or to use higher frequency data acquisition.​19,20

While these solutions represent significant progress, they still fall short of the scale needed for modern research and drug development pipelines, and magnetic force spectroscopy remains inaccessible to those without specialist expertise and equipment.

The key innovations that have allowed us to scale magnetic force spectroscopy

With the MAGNA One instrument and cartridge system, Depixus has transformed magnetic force spectroscopy into an accessible large-scale platform designed to meet the demands of today’s academic and pharma researchers.

Our patented platform overcomes the inherent limitations of conventional magnetic force spectroscopy approaches, delivering unprecedented scale and resolution through four core innovations.

Precisely patterned flow cell array

Depixus MAGNA One’s multi-use cartridge features a regular array of 35,000 microscopic printed spots for precise molecule placement.

This ordered distribution of molecules on the cartridge ensures sufficient separation between beads, preventing interference between beads than are too closely spaced. It also ensures there is no wasted area due to excessive spacing between beads, enabling the density of beads to be increased by about 10-fold compared with random distribution.21

Direct light measurement

Unlike other instruments, bead position in Depixus MAGNA One is determined not by imaging of an optical pattern but rather by direct measurement of light scattered from each bead using Total Internal Reflection (TIR) illumination.

High-intensity laser light is beamed into the transparent floor of the flow cell of the cartridge, creating a large evanescent light field above it, the intensity of which decays exponentially with distance from the surface.

The vertical position of the beads in this light field can be precisely determined from the amount of light that they scatter. Beads closer to the surface will be subject to more intense evanescent field illumination so will scatter more light, while beads further from the surface will be subject to less illumination and scatter less light (Figure 1).

The intensity of the light that is scattered downwards can then be measured using a camera positioned underneath the cartridge to precisely determine the vertical position of each bead.

Figure 1. Schematic showing how Depixus MAGNA One tracks vertical bead position by collecting the evanescent light scattered by each bead.

Precision pixel-bead mapping

One of the most innovative aspects of Depixus MAGNA One that allows scalability is combining the precisely patterned sample array with a highly sensitive complementary metal oxide semiconductor (CMOS) camera, enabling each individual bead to be mapped onto a single pixel (Figure 2).

Figure 2. Example image of pixel illumination mapping in Depixus MAGNA One, with the intensity of each pixel corresponding to the vertical position of a single bead.

To achieve this, the camera must be able to measure very small variations in a relatively bright light and to run at frequencies of tens or hundreds of frames per second to capture dynamic movements with high temporal resolution.

We use a camera with high well-depth that gives linear readings across a wide dynamic range and can cope with intense light. It has a relatively large pixel size of 12 µm x 12 µm which is compatible with the spacing needed between beads to avoid magnetic interactions and crosstalk between pixel signals.

High-performance lensing system

In addition to the camera, a high-performance lensing system ensures accurate collection of the scattered light from each single pixel.

A telecentric machine-vision lens provides low distortion, 1:1 magnification, and the widest possible aperture to collect maximum light. Depixus MAGNA One also features a nanometric focusing device (Z-axis focus) that also allows precise X-Y alignment of the beads to the pixels and minimizes light leakage to adjacent pixels.

These innovations collectively enable Depixus MAGNA One to perform single-molecule analysis of thousands of dynamic biomolecular interactions in parallel in real time.

Delivering high-resolution, large-scale MFS in a user-friendly laboratory instrument

Beyond the technical innovations, there are additional features within Depixus MAGNA One that turn MFS from an inaccessible, specialist technology to an indispensable and versatile laboratory tool.

Unlike other MFS setups that require specialized equipment and technical expertise, Depixus MAGNA One integrates everything into a single, user-friendly platform. An integrated automated fluidics delivery system and highly customizable experimental protocols enable exploration of a wide range of biomolecules and applications.

Raw data is collected automatically and processed using a custom software suite that has been designed to support both the lowest-level exploration of raw data as well as high-level automated and customizable analysis of all pixels, including statistical analysis across populations of molecules.

Advantages and applications of Depixus MAGNA One

The benefits of combining the detail and insights of single-molecule techniques with scalability in a single user-friendly laboratory instrument are profound.

By gathering data streams from thousands of individual molecules, Depixus MAGNA One can reveal heterogeneity within populations and capture weak, transient or rare events that are missed by bulk analysis techniques or unlikely to be seen by observing just a handful of molecules.22

Depixus MAGNA One also provides researchers with insights into the dynamic mechanisms underpinning molecular behavior and interactions, including detailed kinetic and thermodynamic data.

The scale of this data is critical for applications such as the lead selection and optimization phases of drug development, where the ability to simultaneously study thousands of individual interactions in parallel can drastically accelerate workflows.

The versatility of Depixus MAGNA One allows for a wide range of applications, from studying nucleic acid binding enzymes, to exploring RNA-targeted therapeutics or protein-protein interactions.

A new era for molecular interactomics

Depixus MAGNA One redefines what is possible with MFS by making it not only scalable but also accessible for the first time in a laboratory instrument, making it a powerful tool for academic researchers and drug developers alike.

By integrating large-scale capacity and precision with an intuitive user-friendly design, Depixus MAGNA One is poised to accelerate discoveries in molecular biology and biophysics.

To explore in more detail how Depixus MAGNA One™ can be used in your research, download our product brochure today.

References

  1. Smith SB, Finzi L, Bustamante C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 1992;258(5085):1122-1126. doi:10.1126/science.1439819
  2. Strick TR, et al. The elasticity of a single supercoiled DNA molecule. Science. 1996;271(5257):1835-1837. doi:10.1126/science.271.5257.1835
  3. Sarkar R, Rybenkov VV. A guide to magnetic tweezers and their applications. Front Phys. 2016;4:48. doi:10.3389/fphy.2016.00048
  4. Smith SB, Cui Y, Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 1996;271(5250):795-799. doi:10.1126/science.271.5250.795
  5. Liphardt J, Onoa B, Smith SB, Tinoco IJ, Bustamante C. Reversible unfolding of single RNA molecules by mechanical force. Science. 2001;292(5517):733-737. doi:10.1126/science.1058498
  6. Abels JA, Moreno-Herrero F, van der Heijden T, Dekker C, Dekker NH. Single-molecule measurements of the persistence length of double-stranded RNA. Biophys J. 2005;88(4):2737-2744. doi:10.1529/biophysj.104.052811
  7. Ruiz-Gutierrez N, Rieu M, Ouellet J, Allemand JF, Croquette V, Le Hir H. Novel approaches to study helicases using magnetic tweezers. Methods Enzymol. 2022;673:359-403. doi:10.1016/bs.mie.2022.03.035
  8. Maier B, Bensimon D, Croquette V. Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc Natl Acad Sci U S A. 2000;97(22):12002-12007. doi:10.1073/pnas.97.22.12002
  9. Charvin G, Strick TR, Bensimon D, Croquette V. Tracking topoisomerase activity at the single-molecule level. Annu Rev Biophys Biomol Struct. 2005;34:201-219. doi:10.1146/annurev.biophys.34.040204.144433
  10. Manosas M, Spiering MM, Ding F, Croquette V, Benkovic SJ. Collaborative coupling between polymerase and helicase for leading-strand synthesis. Nucleic Acids Res. 2012;40(13)doi:6187-6198. doi:10.1093/nar/gks254
  11. Tapia-Rojo R. Single-molecule magnetic tweezers to unravel protein folding dynamics under force. Biophys Rev. Published online 2025. doi:10.1007/s12551-025-01274-1
  12. Bauer MS, Gruber S, Hausch A, et al. Single-molecule force stability of the SARS-CoV-2-ACE2 interface in variants-of-concern. Nat Nanotechnol. 2024;19(3):399-405. doi:10.1038/s41565-023-01536-7
  13. Bonakdar N, Schilling A, Spörrer M, et al. Determining the mechanical properties of plectin in mouse myoblasts and keratinocytes. Exp Cell Res. 2015;331(2):331-337. doi:10.1016/j.yexcr.2014.10.001
  14. Bausch AR, Möller W, Sackmann E. Measurement of local viscoelasticity and forces in living cells by magnetic tweezers. Biophys J. 1999;76(1 Pt 1):573-579. doi:10.1016/S0006-3495(99)77225-5
  15. Ribeck N, Saleh OA. Multiplexed single-molecule measurements with magnetic tweezers. Rev Sci Instrum. 2008;79(9):94301. doi:10.1063/1.2981687
  16. Rieu M, Vieille T, Radou G, et al. Parallel, linear, and subnanometric 3D tracking of microparticles with Stereo Darkfield Interferometry. Sci Adv. 2021;7(6). doi:10.1126/sciadv.abe390
  17. Agarwal R, Duderstadt KE. Multiplex flow magnetic tweezers reveal rare enzymatic events with single molecule precision. Nat Commun. 2020;11(1):4714. doi:10.1038/s41467-020-18456-y
  18. Johnson KC, Clemmens E, Mahmoud H, Kirkpatrick R, Vizcarra JC, Thomas WE. A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control. J Biol Eng. 2017;11:47. doi:10.1186/s13036-017-0091-2
  19. Dulin D, Cui TJ, Cnossen J, Docter MW, Lipfert J, Dekker NH. High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics. Biophys J. 2015;109(10):2113-2125. doi:10.1016/j.bpj.2015.10.018
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