DNA Nanotechnology

DNA is the carrier of hereditary information and therefore a central component of all life on earth. However, due to its unique chemical and structural properties, DNA can also be used as a programmable material for the controlled synthesis of molecularly defined artificial nanostructures. The DNA origami technique enables the fast, high-yield synthesis of 2D and 3D nanostructures by exploiting the strong specificity of Watson-Crick base pairing. It is based on folding a long single-stranded DNA scaffold into a desired shape with the help of hundreds of short synthetic oligonucleotides. This technique provides a straightforward means to assemble user-defined nanostructures with arbitrary, yet well-defined shapes. Furthermore, the unique sequences of the oligonucleotides employed in DNA origami folding enable the resulting DNA origami nanostructures to serve as spatially addressable molecular breadboards for the controlled arrangement of biomolecules and nanoparticles with nanometer precision. We are exploring potential real-world applications of DNA origami technology with a focus on the following application areas.

DNA origami nanostructures can be modified to carry a variety of therapeutic and diagnostic cargos such as enzymes, siRNA, fluorescent dyes, and chemotherapeutic drugs. Furthermore, they can be decorated with recognition sites that may specifically bind to target cells, facilitate cellular uptake, or trigger the release of the cargo. Consequently, they represent promising nanocarriers for drug delivery and targeted therapy. Therefore, we are investigating the stability of DNA origami nanostructures under physiological conditions, their efficient loading with various drugs, and their interaction with biological systems. We are particularly interested in superstructure-dependent effects.

Selected publications:

• Direct visualization of the drug loading of single DNA origami nanostructures by AFM-IR nanospectroscopy, M. Hanke, G. Grundmeier, and A. Keller, Nanoscale 14, 11552 (2022) (Cover Picture)
• Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings, Y. Xin, P. Piskunen, A. Suma, C. Li, H. Ijäs, S. Ojasalo, I. Seitz, M.A. Kostiainen, G. Grundmeier, V. Linko, and A. Keller, Small 18, 2107393 (2022)
• Effect of DNA Origami Nanostructures on hIAPP Aggregation, M. Hanke, A. Gonzalez Orive, G. Grundmeier, and A. Keller, Nanomaterials 10, 2200 (2020)

Due to their high mechanical rigidity and intrinsic biocompatibility, DNA origami nanostructures represent powerful tools for numerous applications in biophysics, ranging from the measurement of inter- and intramolecular forces to single-molecule protein folding and unfolding studies. Since most of these applications, however, rely on an intact and well-defined DNA origami shape, thermal fluctuations and limited stability under relevant conditions become critical factors to consider when conducting such studies on DNA origami substrates. This is further complicated by the fact that DNA origami nanostructures present some unique structural properties including numerous non-natural DNA topologies that may deviate substantially from genomic DNA. We, therefore, investigate the behavior of DNA origami nanostructures under various relevant conditions with special emphasis on their interaction with chemical species such as chaotropic denaturants. 

Selected publications:

• Effect of Ionic Strength on the Thermal Stability of DNA Origami Nanostructures, M. Hanke, E. Tomm, G. Grundmeier, and A. Keller, ChemBioChem (2023)
• Anion-specific structure and stability of guanidinium-bound DNA origami, M. Hanke, D. Dornbusch, C. Hadlich, A. Rossberg, N. Hansen, G. Grundmeier, S. Tsushima, A. Keller, and K. Fahmy, Comput. Struct. Biotechnol. J. 20, 2611 (2022)
• Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate, M. Hanke, N. Hansen, R. Chen, G. Grundmeier, K. Fahmy, and A. Keller, Int. J. Mol. Sci. 23, 2817 (2022)

Many potential applications of DNA origami nanostructures in nanoelectronics, (bio)chemical sensing, lab-on-chip diagnostics, and tissue engineering, rely on their deposition on solid substrates. Furthermore, DNA origami nanostructures immobilized on solid surfaces can also be used as molecular lithography masks to transfer their shapes into various organic and inorganic materials. Therefore, the controlled deposition of single DNA origami nanostructures, as well as their hierarchical self-assembly into ordered 2D lattices represent important steps toward such real-world applications. We are therefore investigating DNA origami adsorption and lattice formation on solid substrates to elucidate the underlying molecular mechanisms. We furthermore utilize adsorbed DNA origami nanostructures for surface functionalization using molecular lithography techniques.

Selected publications:

• Scaling up DNA Origami Lattice Assembly, Y. Xin, B. Shen, M.A. Kostiainen, G. Grundmeier, M. Castro, V. Linko, and A. Keller, Chem. - Eur. J. 27, 8564 (2021) (Frontispiece)
• Self-assembly of highly ordered DNA origami lattices at solid-liquid interfaces by controlling cation binding and exchange, Y. Xin, S. Martinez Rivadeneira, G. Grundmeier, M. Castro, and A. Keller, Nano Res. 13, 3142 (2020)
• Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks, S. Ramakrishnan, S. Subramaniam, A.F. Stewart, G. Grundmeier, and A. Keller, ACS Appl. Mater. Interfaces 8, 31239 (2016)

The unique possibility to arrange functional entities and especially single biomolecules such as proteins and nucleic acids on DNA origami nanostructures with molecular precision enables the synthesis of well-defined biomolecular nanoarrays, that may serve as functional platforms in single-molecule studies. By using high-resolution atomic force microscopy (AFM) to visualize single proteins in such DNA origami-based nanoarrays, we can distinguish and quantify different binding and dissociation events. We are currently applying this technique in the investigation of protein-drug interactions and the discovery of small-molecule protein inhibitors. We also aim at further advancing this concept toward a high-throughput screening assay for fragment-based drug discovery.

Selected publications:

• Arranging Small Molecules with Sub-Nanometer Precision on DNA Origami Substrates for the Single-Molecule Investigation of Protein-Ligand Interactions, J. Huang, A. Suma, M. Cui, G. Grundmeier, V. Carnevale, Y. Zhang, C. Kielar, and A. Keller, Small Struct. 1, 2000038 (2020)
• Quantitative Assessment of Tip Effects in Single‐Molecule High‐Speed Atomic Force Microscopy using DNA Origami Substrates, C. Kielar, S. Zhu, G. Grundmeier, and A. Keller, Angew. Chem. Int. Ed. 59, 14336 (2020)
• Pharmacophore Nanoarrays on DNA Origami Substrates as a Single‐Molecule Assay for Fragment‐Based Drug Discovery, C. Kielar, F.V. Reddavide, S. Tubbenhauer, M. Cui, X. Xu, G. Grundmeier, Y. Zhang, and A. Keller, Angew. Chem. Int. Ed. 57, 14873 (2018)