Single-molecule and single-cell biophysics

To study processes at the level of single molecules and single cells, the tools need to be on the same size scale as the objects under study. We therefore develop micro and nanofluidic devices on scales ranging from tens of nanometers to hundreds of micrometers to manipulate, visualize and sort biomolecules, cells and other bioparticles.

Research areas:

Single-molecule biosensing
Nanoconfined molecules
Label-free sorting of bioparticles ranging from parasites to exosomes
Molecular motors

Single-molecule biosensing

We use nanowire-enhanced surfaces for the detection of fluorescent molecules with extremely high sensitivity, for research and applications.

Principle of Single Molecule Detectionwith nanowires that emit light vertically. Graphics: Phillip Krantz

Semiconductor nanowires can act as nanoscaled optical fibres, enabling them to guide and concentrate the light emitted by surface-bound fluorophores. The efficient light management enables more sensitive optical biosensing.

We explore the physics underlying the mechanism and develop applications in precision diagnostics. An important basis of this work is the Swedish Research Council Research Environment on Single molecule bioanalytical sensing for precision cancer diagnostics funded 2020 – 2025.

The technology is in the process of commercialization through Aligned Bio

Nanoconfined molecules

DNA confined in nanochannels naturally stretches out due to a combination of excluded volume effects and elastic properties of the DNA molecule depending on the size of the channels. This gives us unprecedented opportunities to study the physics of confined polymers, the interaction between DNA and other molecules and the genomics of individual DNA molecules.

One of our main research areas is to develop methods to identify microorganisms. Through the direct visualization of the DNA in the nanochannels together with simple barcoding methods we can do this without any culturing of the cells nor any DNA amplification. This would speed up the diagnosis of infectious disease dramatically compared to standard techniques. It would also allow us to identify any microorganisms that today evade detection due to difficulty of culturing. The work entails development of lab on a chip devices using advanced nano and microfabrication techniques for sample preparation and enrichment, DNA extraction and nanochannels for the visualization of the DNA.

Direct visualization of DNA in nanochannels. (A) An entire chromosome from yeast (S. pombe) is stretched out in a meandering channel. (B) Kymograph of melted DNA. The horizontal axis represents the spatial axis along the stretched DNA and the vertical axis the time. See also Noble C, et al (2015) A Fast and Scalable Kymograph Alignment Algorithm for Nanochannel-Based Optical DNA Mappings. PLoSONE 10(4): e0121905. doi:10.1371/journal.pone.0121905

Label-free sorting of bioparticles ranging from parasites to exosomes

Cell sorting typically takes place based on the fluorescent labelling of molecular markers inside or on the surface of the cells of interest (Fluorescently activated cell sorting, FACS). Although it represents a powerful technology with widespread use, it suffers from several limitations. Due to its relatively high cost, large size and requirement for skilled staff it has poor portability. This often limits its use to central core facilities and makes it difficult to put it to use close to the patient or during field work.

To address these issues and to complement conventional cell-sorting technologies we develop microfluidic label-free sorting schemes based on the inherent properties of cells such as size, deformability, electrical properties and morphology. Our main target is applications in medicine and biomedical research but we are also open for other application areas. The use of simple microfluidic devices will make it possible to extend the use of cell-sorting to the point of care, closer to the patient, at the clinic or in the field.

Device for cell sorting — Microfluidic device for label-free cell sorting. Adapted from Tran et al., Lab on a Chip (2017).

Molecular motors

We explore novel techniques and approaches to studying how molecular motors work, and to develop technical uses of biological motors. Molecular motors are complex protein assemblies (typically tens of nanometers in size) that use chemical energy (ATP) to perform mechanical tasks such as transport within living cells. From a physics point of view, molecular motors are interesting. They function fundamentally differently from macroscopic, man-made machines, for example, they use random, thermal fluctuations (diffusion) as part of their operation. From a technical point of view, molecular motors may eliminate the need for external pumps in lab-on-a-chip applications, allowing extreme miniaturization.

We pursue two key directions of research. In the first, we use a bottom-up approach to help elucidate the engineering principles of molecular motors. Supported by numerical modelling, we aim to construct artificial, bio-molecular motors using building blocks such as proteins and DNA. One advantage of this approach is that our artificial motors are based on relatively simple, well-known designs, making it easier to understand structure-function relationships.

Second, we aim to develop parallel computation using nanofabricated networks that are explored by many self-propelled biological agents, such as actin filaments.
In this area, we coordinate the EU FET Open project Bio4Comp (2017 – 2021)

Key publications

Nanowires for Biosensing: Lightguiding of Fluorescence as a Function of Diameter and Wavelength. D. Verardo, F. Lindberg, N. Anttu, C. Niman, M. Lard, A. Dabkowska, T. Nylander, A. Månsson, Ch. Prinz, H. Linke. Nano Lett. 2018, 18, 8, 4796-4802. https://doi.org/10.1021/acs.nanolett.8b01360
See article nanowires for biosensing at the publisher's site

Single-Molecule Denaturation Mapping of Genomic DNA in Nanoﬂuidic Channels. W.W. Reisner, N.B. Larsen, A. Silahtaroglu, A.Kristensen, N.Tommerup, J. O. Tegenfeldt, H. Flyvbjerg. PNAS 107 (30), 13294-13299 (2010). DOI: 10.1073/pnas.1007081107
See article single-molecule denaturation at publisher's site

Separation of Pathogenic Bacteria by Chain Length J. P. Beech, B. Dang Ho, G. Garriss, V. Oliveira, B. Henriques-Normark, J.O. Tegenfeldt. Analytica Chimica Acta (2018) 1000, 223-23. DOI: 10.1016/j.aca.2017.11.050
See article separation of pathogenic bacteria at publisher's site

Parallel computation with molecular motor-propelled agents in nanofabricated networks D. V. Nicolau Jr., M. Lard, F. van Delft, T. Korten, M. Persson, E. Bengtsson, A. Månsson, S. Diez, H. Linke, D. V. Nicolau. (2016). PNAS, 113 (10), 2591-2596. DOI: 10.1073/pnas.1510825113
See article parallel computation at publisher's site