Periodic Reporting for period 4 - DNA Funs (DNA-based functional lattices)
Reporting period: 2023-10-01 to 2024-09-30
Advances in design and low-cost production of DNA nanostructures allow us to challenge nature in nanoscale positioning. By combining the assembly power of DNA origami with top-down lithography we intend to fabricate functional nanostructured materials designed on the molecular level while reaching macroscopic dimensions. A self-assembly approach to manufacturing has the potential to reduce production costs and increase efficiencies of light- harvesting devices, intelligent surfaces and future computing devices. For the latter, we here intend to develop new building blocks for next-generation all-optical circuits.
Three objectives have been defined:
A: We design and implement DNA structures that are organized on patterned surfaces and assemble into 3D networks that exhibit the highest possible contact area for electron donor and acceptor molecules in self-assembled energy conversion devices.
B: Custom-tailored photonic crystals built from lattices of DNA origami structures will control the flow of light.
C: We create topologically protected edge states in DNA-assembled particle lattices. Such topologically protected states are sought after for the coherent and loss-less propagation of information.
This action has been concluded successfully with the major achievements explained below.
Three objectives have been defined:
A: We design and implement DNA structures that are organized on patterned surfaces and assemble into 3D networks that exhibit the highest possible contact area for electron donor and acceptor molecules in self-assembled energy conversion devices.
B: Custom-tailored photonic crystals built from lattices of DNA origami structures will control the flow of light.
C: We create topologically protected edge states in DNA-assembled particle lattices. Such topologically protected states are sought after for the coherent and loss-less propagation of information.
This action has been concluded successfully with the major achievements explained below.
Objective A focused on leveraging DNA origami for precise nanoscale positioning in three dimensions, enabling new approaches to light energy harvesting. A key advancement was integrating three-dimensional DNA origami designs onto nanopatterned substrates. A subsequent silicification process produced hybrid DNA–silica structures with superior mechanical and chemical stability, reaching the sub-10-nm regime and allowing precise integration of inorganic and organic components (published in: Martynenko et al., "Site-directed placement of three-dimensional DNA origami" Nature Nanotechnology 2023).Our nanotexturing method enables the development of complex three-dimensional surfaces and integrated devices, opening possibilities for advanced energy-harvesting designs. Additionally, we combined these results with self-assembling surface patterning techniques using colloidal nanoparticles, effectively replacing time-intensive top-down lithography.
In parallel, we developed a fabrication technique for conformally coating DNA origami frameworks and chip designs with functional metal oxides via atomic layer deposition (ALD). This method preserves the DNA framework’s integrity while enabling tunable nanometer-thin layers of functional materials like ZnO, TiO2, and IrO2. Notably, our approach facilitated electrocatalytic water splitting using IrO2-coated DNA origami frameworks, exhibiting drastically improved performance over planar films (Ermatov et al., "Fabrication of functional 3D nanoarchitectures via atomic layer deposition on DNA origami crystals", JACS 2025). These results highlight DNA origami’s potential as a robust platform for engineering interpenetrating, 3D nanomaterials with precise topologies and material compositions for energy conversion.
In Objective B, our key breakthrough was the demonstration of DNA-based photonic crystals (Posnjak et al., "Diamond-lattice photonic crystals assembled from DNA origami", Science 2024). We assembled DNA origami-based building blocks into a rod-connected 3D lattice. Using DNA origami tetrapods that acted as "quasi-carbon atoms", we designed a cubic diamond lattice with a periodicity of 170nm, which, after ALD with a high-refractive-index material such as TiO2, enabled tunable photonic bandgaps in the near-UV. Additionally, we used DNA origami crystals as scaffolds for plasmonic particles, creating lattices exhibiting unique light-matter interactions. Chiral origami-based meta-molecules were assembled into chiral plasmonic crystals carrying nanoparticles, yielding strong circular dichroism (Sikeler et al., "Chiral Plasmonic Crystals Self-Assembled by DNA Origami", J. Phys. Chem. C 2025).
Another success was the development of a DNA origami-based reconfigurable optical switch. This system leveraged single-to-double-stranded DNA transitions to generate entropic forces, leading to large-scale plasmonic particle motion and enabling DNA-controlled optical responses (Gür et al., "Double‐to Single‐Strand Transition Induces Forces and Motion in DNA Origami Nanostructures", Advanced Materials 2021). Our DNA nanostructures can thus serve as dynamic, reconfigurable photonic components, advancing the integration of nanoscale motion into optical devices.
A significant achievement within Objective C was the fabrication of plasmonic metasurfaces through DNA origami self-assembly and electron beam lithography, allowing deterministic positioning of gold nanospheres on SiO2 surfaces to form precisely structured metasurfaces with tunable optical responses (Sikeler et al., "DNA Origami‐Directed Self‐Assembly of Gold Nanospheres for Plasmonic Metasurfaces", Adv. Funct. Mat., 2024).
Fulfilling the core promise of this objective, we then fabricated a zigzag chain of gold nanospheres to replicate the plasmonic Su-Schrieffer-Heeger (SSH) model (Christoph Sikeler, PhD thesis, LMU). This system enabled direct visualization of topologically protected edge states that were tunable by rotating a linear polarization filter, with experimental observations aligning closely with theoretical predictions.
In conclusion, our team demonstrated groundbreaking achievements in light manipulation and energy conversion through DNA origami. By harnessing the precision of DNA self-assembly, we developed innovative fabrication methods, enhanced photonic crystal architectures, and introduced topologically protected states with direct implications for all-optical circuits. These results lay the foundation for future advances in nanophotonics, energy-efficient optical materials, and quantum science.
In parallel, we developed a fabrication technique for conformally coating DNA origami frameworks and chip designs with functional metal oxides via atomic layer deposition (ALD). This method preserves the DNA framework’s integrity while enabling tunable nanometer-thin layers of functional materials like ZnO, TiO2, and IrO2. Notably, our approach facilitated electrocatalytic water splitting using IrO2-coated DNA origami frameworks, exhibiting drastically improved performance over planar films (Ermatov et al., "Fabrication of functional 3D nanoarchitectures via atomic layer deposition on DNA origami crystals", JACS 2025). These results highlight DNA origami’s potential as a robust platform for engineering interpenetrating, 3D nanomaterials with precise topologies and material compositions for energy conversion.
In Objective B, our key breakthrough was the demonstration of DNA-based photonic crystals (Posnjak et al., "Diamond-lattice photonic crystals assembled from DNA origami", Science 2024). We assembled DNA origami-based building blocks into a rod-connected 3D lattice. Using DNA origami tetrapods that acted as "quasi-carbon atoms", we designed a cubic diamond lattice with a periodicity of 170nm, which, after ALD with a high-refractive-index material such as TiO2, enabled tunable photonic bandgaps in the near-UV. Additionally, we used DNA origami crystals as scaffolds for plasmonic particles, creating lattices exhibiting unique light-matter interactions. Chiral origami-based meta-molecules were assembled into chiral plasmonic crystals carrying nanoparticles, yielding strong circular dichroism (Sikeler et al., "Chiral Plasmonic Crystals Self-Assembled by DNA Origami", J. Phys. Chem. C 2025).
Another success was the development of a DNA origami-based reconfigurable optical switch. This system leveraged single-to-double-stranded DNA transitions to generate entropic forces, leading to large-scale plasmonic particle motion and enabling DNA-controlled optical responses (Gür et al., "Double‐to Single‐Strand Transition Induces Forces and Motion in DNA Origami Nanostructures", Advanced Materials 2021). Our DNA nanostructures can thus serve as dynamic, reconfigurable photonic components, advancing the integration of nanoscale motion into optical devices.
A significant achievement within Objective C was the fabrication of plasmonic metasurfaces through DNA origami self-assembly and electron beam lithography, allowing deterministic positioning of gold nanospheres on SiO2 surfaces to form precisely structured metasurfaces with tunable optical responses (Sikeler et al., "DNA Origami‐Directed Self‐Assembly of Gold Nanospheres for Plasmonic Metasurfaces", Adv. Funct. Mat., 2024).
Fulfilling the core promise of this objective, we then fabricated a zigzag chain of gold nanospheres to replicate the plasmonic Su-Schrieffer-Heeger (SSH) model (Christoph Sikeler, PhD thesis, LMU). This system enabled direct visualization of topologically protected edge states that were tunable by rotating a linear polarization filter, with experimental observations aligning closely with theoretical predictions.
In conclusion, our team demonstrated groundbreaking achievements in light manipulation and energy conversion through DNA origami. By harnessing the precision of DNA self-assembly, we developed innovative fabrication methods, enhanced photonic crystal architectures, and introduced topologically protected states with direct implications for all-optical circuits. These results lay the foundation for future advances in nanophotonics, energy-efficient optical materials, and quantum science.
Our work on diamond-lattice photonic crystals assembled from DNA origami advanced various fields. First, it demonstrated to what level of material complexity DNA self-assembly can be driven. Single-crystals with diameters of up to 50 µm were assembled from ~ 10 Million DNA origami structures, each only 70 nm small. Second, we assembled the first rod-connected cubic diamond lattice, an achievement by itself for the crystal community. Finally, our crystals' lattice spacing in combination with the material parameters gave rise to a photonic band gap in the near UV.
Achieving site-directed placement of three-dimensional DNA origami is remarkable for several reasons: (i) 3D (thus far only 2D) DNA origami structures can now be positioned on substrates with nanometer accuracy. (ii) The patterning works with electron-beam lithography but also with sphere-lithography, where spheres self-assembling on the substrates form the mask for downstream chemical processing of the surface. (iii) Gold nanoparticles can be placed with nanometer precision at defined distances from the substrate.
The combination of plasmonic nanoparticles with DNA origami surface patterning enabled further milestones such as DNA-directed assembly plasmonic metasurfaces, topologically protected edge states and self-assembled plasmonic physical unclonable functions, i.e. substrates that give a unique optical response that can not be copied by anyone, not even ourselves, making this ultra-secure cryptography or product safety features.
Achieving site-directed placement of three-dimensional DNA origami is remarkable for several reasons: (i) 3D (thus far only 2D) DNA origami structures can now be positioned on substrates with nanometer accuracy. (ii) The patterning works with electron-beam lithography but also with sphere-lithography, where spheres self-assembling on the substrates form the mask for downstream chemical processing of the surface. (iii) Gold nanoparticles can be placed with nanometer precision at defined distances from the substrate.
The combination of plasmonic nanoparticles with DNA origami surface patterning enabled further milestones such as DNA-directed assembly plasmonic metasurfaces, topologically protected edge states and self-assembled plasmonic physical unclonable functions, i.e. substrates that give a unique optical response that can not be copied by anyone, not even ourselves, making this ultra-secure cryptography or product safety features.