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Liedl Group

Welcome to the Liedl Research Group on Molecular Self-Assembly and Nanoengineering

We are interested in molecular self-assembly processes in general and particularly in the engineering of functional DNA devices using the DNA origami method. We will focus on the integration of self-assembled DNA nanostructures with lithographically defined environments. We hope to combine well-established lithography methods with the advantages of self-assembly and molecular addressability. The design of functional DNA hybrid materials and its characterization will also help us to understand the mechanical and chemical interactions across multiple levels of organization between the different molecular components in living cells and tissues.

We are grateful to funding from the European Research Council (ERC) enabling us to realize the ERC Consolidator Grant project DNA-Funs: DNA-based functional lattices (link)

Wer are a member lab of the Munich DNA Node.

Master’s Thesis Projects
Project : DNA origami-based photonic crystal

 3d dna origami crytal.jpg

We are looking for a motivated masters student to work on a project aimed at creating a DNA origami-based photonic crystal. Photonic crystals are structures with periodic variation of refractive index on scales smaller than the wavelength of visible light. Their ordered structure leads to optical properties analogous to electric properties of semiconductors, namely only light with certain frequencies can propagate through the material, which enables novel ways to control light. DNA origami is uniquely suited as a material to assemble photonic crystals as it offers programmable assembly on a scale of tens of nanometers. As with all cutting-edge research, there are many open paths to explore, so the exact direction of research for a masters thesis will be determined together with the candidate.

You will learn:
- DNA origami
- TEM and SEM microscopy
- deposition of different materials on DNA origami
- spectroscopy and scattering measurements
If you are interested, please contact Gregor (Gregor.Posnjak@physik.uni-muenchen.de) or Tim Liedl (tim.liedl@physik.lmu.de).

Project : Deterministic placement of DNA Origami structures

dna origamistructures

Top-down nanolithography utilizes the placement of features at predefined positions to create nanodevices. However, it is still limited by its resolution as well as its inability to place single molecules with accuracy. DNA Origami utilizes bottom-up self-assembly to achieve ~ 1 nm resolution in the placement of single molecules. Based on recent works, we achieved deterministic placement of DNA Origami structures on various substrates (‘Deterministic placement’ figure, bottom right). This opens up applications ranging from photovoltaic devices to sensing.
In this project, the candidate would learn DNA origami placement and develop new protocols to create more complex patterns that can be tuned depending on the application, like plasmonic nanodevices or single-molecule biosensing. Since this is a novel research problem, there is ample opportunity to design independent research problems with the candidate for the thesis.
You will learn :
- DNA origami design and self-assembly
- analytical techniques like scanning electron microscopy (SEM) and Atomic Force Microscopy (AFM)
- nanofabrication techniques like electron-beam evaporation and lithography.
There will be opportunities to work in both a wet lab as well as a cleanroom.
If you are interested, write to Mihir (Mihir.Dass@physik.uni-muenchen.de) or Tim Liedl (tim.liedl@physik.lmu.de).

DNA Origami

DNA Origami Concept

The achievable complexity of man-made DNA structures has taken a great leap forward with the recent invention of 2D DNA origami by Paul Rothemund (Rothemund, P. W. K., Nature, 2006). This technique employs a virus-based DNA single strand (7 kb long) as a scaffold which is brought into shape by hundreds of short oligonucleotides. In 2009 we have shown in the group of William Shih that this method can be extended to three dimensions and that arbitrary nanoscale shapes can be realized (Douglas, S. M. et al., Nature, 2009). These three-dimensional (3D) DNA origami structures can multimerize into rigid objects spanning micrometers in length while they are addressable with nanometer precision.

The fine positional accuracy offered by 3D DNA origami nanostructures will help us bridge the gap between the macroscopic and the nanoscopic world and will enable us to investigate biomolecular (model) systems at unprecedented levels of control. Please find below a few of the research topics pursued in our lab.

Current Research Interests:

3D DNA Origami Crystals

crystalThus far, arranging sizeable guest molecules in three dimensions using DNA frameworks has not been achieved, mainly because the reported DNA lattices either lack the possibility to grow in three dimensions, or lack sufficient rigidity and / or cavity size to host guest molecules. Here we overcome these challenges and show the poly-crystalline assembly of a DNA origami-based triangular tensegrity structure into rhombohedral lattices and we further demonstrate our capacity to co-crystallize even large guest nanocomponents by using gold nanoparticles of various sizes.

  • T. Zhang, C. Hartl, K. Frank, A. Heuer-Jungemann, S. Fischer, P. C. Nickels, B. Nickel, T. Liedl
    3D DNA Origami Crystals
    Advanced Materials 30, 1800273 (2018) 

Molecular Force Spectroscopy with a DNA Origami-Based Nanoscopic Force Clamp

force_clamp_holliday_junctionWe have constructed self-assembling, nanoscopic force clamps to study biomolecules under constant, adjustable forces in the low picomolar range. The self-assembled devices act fully autonomously as no physical connections to the outside world, such as long tethers and surfaces, are required. Optical reporting allows accurate detection of molecular fluctuations at millisecond resolution and under adjustable forces. Instead of creating forces “artificially” through optical or magnetic traps or by pulling with AFM cantilevers, the forces in our system are generated through the statistical fluctuations / entropic spring behavior of a biomolecule that is nanoscopic itself. The nanoscopic size and the easy manufacturing of DNA origami structures that self-assemble at high yields results in massive parallelization of measurements and high data throughput.

Magnetic Propulsion of Microswimmers with DNA-Based Flagellar Bundles

MicroswimmersMany microorganisms use appendages, so-called flagella, to swim or propel through viscous environments. By imitating these microstructures, artificial microswimmers with promising applications in fields ranging from biomedical health care (e.g. drug delivery) to non-equilibrium physics (e.g. swarming) can be constructed. DNA-based self-assembly presents a promising new route for this endeavour as it offers the advantage of a systematic design, large scale production and straightforward functionalization.

DNA-Assembled Nanoparticle Rings Exhibit Electric and Magnetic Resonances at Visible Frequencies

Nanoparticle RingsTailored optical properties in the visible frequency range can be achieved by the precise arrangement of plasmonic nanoparticles on the nanometer scale. With the help of DNA origami we built template structures for metal nanoparticles exhibiting electric responses and artificial optical magnetism. The unique plasmonic features of such artificial metamolecules are examined on the single-object level by using scattering spectroscopy as well as on the ensemble level by absorption spectroscopy.

 



DNA-based Self-Assembly of Fluorescent Nanodiamonds

Nanodiamonds

Fluorescent nanodiamonds (FNDs) containing nitrogen-vacancy centers have attracted much attention as a new class of stable fluorescent markers and as promising candidates for spin-based quantum technologies. So far, however, ineffective surface functionalization of FNDs has been a serious barrier to FND handling and their wider application. Here we have developed a novel and reliable surface modification method by using a PEG-labeled biopolymer as stable coating molecule and assembled these functionalized FNDs in predefined geometries with the help of DNA origami. Optical studies confirmed that the fluorescence properties of the N-V centers in our FNDs are preserved during surface modification and DNA assembly. In principle, our work allows constructing highly ordered FNDs arrays or heterostructures to study spin-spin interactions as well as for in vivo optical imaging and labeling applications.

Hierarchical Assembly of Metal Nanoparticles, Quantum Dots and Organic Dyes Using DNA Origami Scaffolds

Planet-Satellite-ModelOne of the aims of nanotechnology is the precise control over spatial arrangements of functional nanoscale elements, such as metal or semiconductor nanoparticles and fluorescent organic molecules. In the correct spatial context, these building blocks can be used to study fundamental physical effects or to convert light into charge oscillations and to transfer energy from one location to another. In the long run, we hope to find ways to mimic nature’s success in building efficient energy-funneling and light-conversion nanoconstructs. We have created self-assembling nanscopic scaffolds out of DNA, which are used to organize all the building blocks mentioned above into functional nanoclusters that have a planet-satellite type structure. This means, a central nanoparticle – the planet – is surrounded by a controllable number of other building blocks – the satellites – at exactly defined distances. 

Nanoscale Structure and Microscale Stiffness of Nanotubes

Nanoscale Structure and Microscale Stiffness of NanotubesBecause of their micrometer scale length and nanometer scale diameter, DNA nanotubes mechanically behave very similar to the molecular filaments that form the cytoskeleton in living cells. In recent years, researchers have developed several strategies to construct DNA nanotubes of various shapes and sizes and decorate them with functional materials such as fluorescent silver clusters or gold nanoparticles.

Thus DNA nanotubes are great model systems for the mechanical properties of biological filaments and are highly promising for the construction of complex functional materials.

We have now studied the relations between the nanometer scale structure and micrometer scale stiffness of DNA nanotubes. Long-range thermal deformations were imaged in real time by fluorescence microscopy, and nanoscopic twist of the DNA structures was visualized with 5 nm gold particles attached to the outside of the tubes. In accordance with an earlier study, we find high bending but low twisting stability. This unusual behaviour can be understood in terms of an elasticity model that takes into account the flexibility of the DNA double helices themselves, as well as that of the single-stranded cross-overs between them.

Plasmonic Nanostructures based on DNA

Plasmonic DNA NanostructuresWe demonstrated the fabrication of self-assembled nanoscopic material that has strong optical activity in the visible range. With the help of 3D DNA origami, we spatially arranged plasmonic nanoparticles (NPs) into nanoscale helices. As a collective optical response emerging from our nanostructures in solution, we detect pronounced circular dichroism (CD) originating from the plasmon-plasmon interactions in the NP helices. The effect is non-directional and also switchable between left- and right-handed orientations by design. Through electroless metal deposition the optical response of the nanohelices can be enhanced drastically. We show that the CD can be tuned by composition of the deposited metal and by mixing of helices composed of different metals. Our results demonstrate the generic potential of DNA origami for assembly of plasmonic metafluids with optical properties defined by design.

Molecular carrier systems based on DNA Nanotechnology

DNA Origami Carrier SystemDNA is usually known as the genetic code for protein synthesis in all living organisms. The application of DNA as a molecular building block on the other hand, allows for the construction of sophisticated nanoscopic shapes that are built entirely from DNA. The outstanding advantage of DNA-based self assembly is that during a single fabrication process billion exact copies of the designed DNA nanostructure are produced in parallel. We developed a DNA origami construct that serves as a carrier system to selectively stimulate immune responses of living cells. Together with the group of Carole Bourquin from Klinik Innenstadt the systematic immune stimulatory effect and the potential cytotoxicity of these DNA nanostructures were investigated. Our innate immune system can detect invasive organisms via a specific DNA motif, the so called CpG sequences, that are prevalent in viruses and bacterias. Endosomal receptors like the Toll-Like Receptor 9 (TLR-9) recognize these CpG sequences when they are internalized by certain immune cells and subsequently activate the immune system. Verena Schüller and her colleagues decorated a DNA origami construct with artificial CpG sequences and used it as an efficient non-toxic carrier system into cells. They demonstrated a selective immune stimulating effect of the DNA complexes by measuring the interleukin secretion of the cells as an indicator for immune activation.

Metalization of DNA origami structures

Metalized DNA Origami StructureRobert Schreiber and Susanne Kempter were able to show with the help of many others in our group, that DNA origami structures of any shape can be easily metalized. They developed a new metalization protocol based on the electrostatic absorption of positively charged gold nanoparticles (1.4 nm in diameter) to the negatively charged backbones of DNA double strands. By electroless deposition of further gold from solution, nanoparticle-seeded DNA constructs were transformed into continuously metalized objects. In our experiments we demonstrated the formation of gold rods of controlled length, DNA-tensegrity-based crosses, nanocuboids and nanodonuts. 

Tensegrity and Mechano-transduction

DNA TensegrityTensegrity - a fusion of the words tension and integrity - is a building principle that is based on the balanced distribution of continuos tension over a structure composed from compression-resistant elements connected by tension bearing components. Such tensed networks exhibit remarkable features such as high overall stability and the potential of reorganization and self-stabilization during and after external distortions while relatively small amounts of material are needed for their assembly. On the cellular level, the tensegrity model suggests that mechanical stresses acting on surface receptors that physically couple the cytoskeleton to the extracellular matrix can be translated into a sudden behavioral response of the cell since a local distortion can be propagated immediately over a whole tensed structure. We have succeeded in building such prestressed three-dimensional tensegrity structures from DNA. For this endeavor we build compression resistant struts using the DNA origami method and connected the ends of the struts with long unpaired regions of ssDNA that act as entropic springs. This way we are able to create networks of controllable geometry and tension.

Functionalization of DNA origami structures

Functionalized DNA Origami StructureUsing the DNA origami approach we are now able to manufacture nanoscale objects of desired shapes which potentially offer a wide range of (bio-)chemical groups with defined position and orientation in space. We can exploit this technique to specifically functionalize DNA nanostructures with metal nanoparticles and organic or inorganic fluorophores. The assembly of partly metallized DNA structures which exhibit fluorophores at designated positions will be pursued in order to gain insight in energy transfer and energy funneling processes.

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