Exploring the potential of DNA-based materials Using DNA as a synthetic material offers the unique opportunity to precisely control the spacing of functional molecules like proteins or antibodies, which can help researchers gain a deeper understanding of cellular function and communication at the bio-interface. Researchers in the InActioN project are using DNA-based nanomaterials to investigate cellular activation mechanisms within the immune system, as Professor Maartje Bastings explains. The primary advantage of using DNA as a material platform is that the molecular interactions are coded by a base pairing, with the result that all the particles are automatically perfect clones of one another. This means that the particles are uniform, there is no heterogeneity, which differentiates DNA from other platforms. “Heterogeneity can be a problem with other material classes,” explains Professor Maartje Bastings, head of the Programmable Biomaterials Laboratory (PBL) at EPFL in Lausanne. As the Principal Investigator of the EU-funded InActioN project, Professor Bastings is now using DNA-based nanomaterials to investigate the importance of spacing and geometry in certain natural processes. “In particular, we’re looking at intracellular immune signalling, the
activation of cells that belong to the immune system,” she outlines. This project builds on Professor Bastings earlier work to control the stability of DNA materials in the biological context. Naturally, DNA is found only in a cell nucleus, and cells have mechanisms in place to destroy what they see as foreign DNA when it is found outside the nucleus. “These destructive forces are inherently present in cells and cellular environments to prevent a potential infection. We have to face these hurdles if we want to use the advantages of DNA as a material platform,” says Professor Bastings. In her earlier research Professor Bastings helped develop methods and engineering strategies to circumvent these problems. “We are now able to engineer the artificial
synthetic DNA particles so that they have a protective coating,” she explains. “With these discoveries, we are now able to use these DNA-based materials to engineer spatially and geometrically controlled biomaterials.”
Folding DNA The project’s research involves manipulating and folding DNA into new geometries, then exploring the impact of this on controlled cellular uptake and subsequent immune cell activation. Professor Bastings draws a parallel with the assembly of lego bricks. “You can’t change the shape of a lego brick. In our project, the lego brick is the DNA, and there are some parameters that are not changeable. The width of the DNA helix is 2 nanometres for example, and there are 10 nucleotides
Schematic representation of how the differential organisation of similar building blocks may result in cellular activation or not, depending on the correct presentation of interacting molecules to their specific counterparts inside a cell.
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per turn,” she says. While these parameters cannot be changed it is possible to rearrange synthetic DNA in other ways, although there are certain rules that need to be followed. “You have to use all of the bricks – the DNA – but you get to use them in quite a free way,” continues Professor Bastings. “If you give the same batch of bricks to 10 different people, you’ll get different designs and geometries, but the content is the same.” Researchers are now able to design a set of bricks that come together into a particle with a certain geometry and mechanical profile, which enables Professor Bastings and her colleagues to control the spacing of functional molecules that can be incorporated via specific interaction with the DNA bricks. Each of the final molecules is still the same, but the location and structural flexibility of the active group can be systematically changed. “We are looking at whether the spacing and flexibility of these molecules, introduced by using DNA, can be used as a regulatory metric of cell activation,” outlines Professor Bastings. The location of the molecules and the ligands depends on the immune signalling pathway
InActioN
Materials engineering
Project Objectives
This research could encourage a shift of approach in materials engineering, with Professor Bastings aiming to show that the geometry and flexibility of a material at the nanoscale can have a significant impact on the selective interaction between materials and cells. Uniform, precisely engineered materials could in future be used to provoke a specific immune response, depending on the specific circumstances, while Professor Bastings believes the project’s work also holds wider relevance. “Our findings are relevant for all ligand-receptor interactions. This opens up a whole new platform of material design for nano-therapeutics,” she says. These signalling pathways can be finely activated or inhibited by materials, which could also lead to deeper insights into how cell signalling works. “We can look from a biophysical and structural mechanics viewpoint at how viruses or cancer cells evade certain signalling pathways,” outlines Professor Bastings.
We are looking at whether the spacing of these molecules, introduced by using DNA, is a regulatory metric of cell activation. that researchers want to activate; Professor Bastings has selected two pathways at two different organelles in a cell. “One pathway happens in the endosome (TLR9), another takes place in the cytoplasm (cGAS-STING). The TLR9 pathway is a pro-inflammatory activation cascade,” she explains. A paper has been published in which Professor Bastings and her colleagues have shown the critical role of geometry and negative influence of flexibility on the spatial positioning of ligands within this TLR9 pathway, and shown that precisely engineered nanomaterials can be highly effective tools in immune stimulation and cellular communication. The cGAS-STING pathway is proving more challenging, with researchers working on how to get the material into the cytoplasm, which lies at the centre of a cell. “The challenge is to find ways of getting these materials to the right place while keeping all the bricks at the right predesigned position,” says Professor Bastings. It’s more difficult to get into the cytoplasm than the endosome, and Professor Bastings says there are still more hurdles to overcome in this part of her research. “With the cytoplasm, the nanomaterials have to escape the endosome,” she explains. “The challenge
EU Research
lies in not damaging the DNA during that process, and we are exploring ways to do it.”
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A virus might evade immune signalling pathways by presenting their active molecules in a different spacing or pattern for example, and the project’s research could play a role in uncovering these kinds of fundamental biology insights. The more immediate priority however is to investigate questions around the delivery of these materials, the organellespecific stability, and the proof-of-concept of spatially and geometrically controlled engineering. “We are making progress in this respect. On the way, however, we may find something that could really revolutionise diagnostics, in which case we will look into more translational activities, which would require further funding,” says Professor Bastings. “We can see that our method is working, so there will certainly be follow-up work in the future.” The primary focus in the project has been on cellular interactions within the immune system, yet Professor Bastings says the relevance of their research is not limited solely to this context. Spatially-controlled, DNAbased materials could also be applied in other scenarios, believes Professor Bastings. “We can adopt the same approach to any situation where there are interactions between two (or more) molecules,” she says.
Intracellular Action of DNA-based Nano-materials The breakthrough of this ERC proposal is to use geometry of nanomaterials as sole parameter to organize intracellular immunological checkpoints into active or inhibitive state. Based on a geometric rearrangement of identical building blocks, we provoke immune activation or inhibition exclusively by variation in spatial organization of proteins. The same material can thus be agonist and antagonist depending on the organization of molecular components. Hereby, we demonstrate that a precise control over geometry can define the potency of immunomodulating materials, pioneering geometry-based immune-engineering.
Project Funding
ERC, Starting Grant € 1 499 755
Project Participants
• Hugo Rodriguez Franco • Pauline Hendrickx • Dr. Marianna Koga • Dr. Jorieke Weiden
Contact Details
Project Coordinator, Prof. Maartje M.C. Bastings École Polytechnique Fédérale de Lausanne (EPFL) Institute of Materials (IMX) Programmable Biomaterials Laboratory (PBL) EPFL - STI - IMX - PBL Station 12 CH-1015 Lausanne, Switzerland T: +41 21 69 32669 E: maartje.bastings@epfl.ch W: pbl.epfl.ch W: https://bastingslab.com Comberlato et al NanoLetters (2022) Koga et al Biomacromolecules (2022) Prof. Maartje M.C. Bastings
Prof. Maartje Bastings is the head of the Programmable Biomaterials Laboratory at EPFL in Lausanne. She specializes in the design of DNA-based supramolecular materials to explore the importance of structural mechanics and precise control of valency and patterns on directional interactions and self-assembly.
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