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Previously Published Results.

We develop novel scientific devices and methods for applications in biomolecular physics, biological chemistry, and molecular medicine. To this end, we currently focus on using DNA as a programmable construction material for building nanometer-scale devices with atomically precise features. We also customize proteins and create and study hybrid DNA-protein complexes. 3D transmission electron microscopy, atomic force microscopy, and single molecule methods such as optical trapping and fluorescence microscopy are among our routine analysis tools. A few words on biomolecular nanotechnology and its benefits can be found here. Below we briefly describe some previously published results. Did you check our current directions?


Folding DNA into twisted and curved nanoscale shapes.

Curved Shapes H Dietz, SM Douglas, and WM Shih.
The ability to engineer complex shapes to custom specification likely will be as critical in realization of advanced functionality for nanoscale technology as it has been for macroscale technology. We used targeted insertions and deletions of base pairs in DNA double helices bundled as a crystal-like array to implement twisting of either handedness and to induce quantitatively controlled bending with radius of curvature as tight as only six nanometers. We also combined multiple curved elements to build diverse nanostructures such as a wireframe beach ball or square-toothed gears. Our new methods provide access to a rich diversity of shapes on the nanoscale. Scale bars: 20 nm. Published in Science, 2009: [pdf] [Perspectives].
Featured in the New York Times and on MSNBC. Download [Podcast].


Self-assembly of DNA into three-dimensional nanoscale shapes.

Straight 3D origamiSM Douglas, H Dietz, T Liedl, B Hogberg, F Graf, and WM Shih.
Molecular self-assembly offers a 'bottom-up' route to fabrication with subnanometre precision of complex structures from simple components. DNA has proved to be a versatile building block for programmable construction of such objects, including two-dimensional crystals, nanotubes, and three-dimensional wire-frame polyhedra. Templated self-asssembly of DNA into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase 'scaffold strand' that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide 'staple strands'. Here, we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six different shapes with dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and heterotrimeric wireframe icosahedra. We anticipate that our methods will provide a general route to the manufacture of sophisticated devices bearing features on the nanometre scale. Scale bars: 20 nm. Published in Nature, 2009: [pdf] [News and Views]. Featured in the Wall Street Journal.


Elastic bond network model for protein unfolding mechanics.

Protein strain networks H Dietz and M Rief.
Recent advances (see below and also the work by Carrion-Vazquez et al (2003, Nat Struct Biol) and by Brockwell et al (2003, Nat Struct Biol)) in single molecule mechanics have made it possible to investigate the mechanical anisotropy of protein stability in great detail. Quantitative prediction of protein unfolding forces at experimental time scales has so far been difficult. In this study we explored the potential of an elastically bonded network model to describe the mechanical unfolding forces of green fluorescent protein in eight different directions of force application. The combination of an elastic network and irreversible bond fracture kinetics offers a new concept to understand the determinants of mechanical protein stability. Published in Physical Review Letters, 2008: [pdf].


Protein Structure by mechanical triangulation.

Protein structure by mechanical triangulation H Dietz and M Rief.
For proteins whose structures resist analysis by conventional means, such as crystallography, NMR, or computer simulation, we explored the potential of a mechanical single molecule technique. Chemical groups inserted at selected locations in protein sequence are used to connect several of the target proteins into long chains. Pulling the chains taut with an atomic force microscope induces unfolding of the portion of the protein between crosslinks. Measuring the change in length upon unfolding allows to conclude precisely on the initial separation of the crosslinking groups in the folded protein. Repeating this for different pairings of three crosslinking points allows for triangulation of the absolute position of individual amino acids in a protein's folded structure. Measurements on GFP closely agreed with crystallographic data. Published in PNAS, 2006: [pdf] [Research Highlight].


Three-dimensional protein stability maps.

Protein Stability Maps H Dietz and M Rief.
The biological function of proteins depends critically on the mechanics and conformational dynamics of their functional, folded structures. The mechanical properties of folded protein structures are still largely unknown. Technical reasons have limited experimental access to mostly only one direction of force application. Knowledge of the full, 3d mechanics of folded protein structures is essential for better understanding how proteins do their work. In this project we combined cysteine engineering with single molecule force spectroscopy to explore the mechanical properties of functional protein structures in 3d. Experiments with GFP revealed a striking anisotropy in the mechanical properties of the functional GFP structure. Published in PNAS, 2006: [pdf].


Exploring the energy landscape of GFP by single-molecule mechanical experiments.

GFP as a force sensor? H Dietz and M Rief.
Green Fluorescent Protein (GFP) has become a workhorse of the cell biologist because it emits bright fluorescence that reveals the locations of molecules or changes in calcium or protein concentration. GFP fluorescence is intimately coupled to its intact folded structure. We explored the potential for using GFP as a clonable in vivo molecular force sensor that reports on forces via loss of its fluorescence signal. Single molecule force spectroscopy by AFM was used to investigate the mechanical stability of the GFP barrel when loaded via its N-C termini. We found a rather complex relation of force to extension, reflecting subsequent population of several partially folded intermediate states. GFP as a force sensor is sensitive for forces above 35 pN. Forces above this threshhold induce rapid decay of the native GFP structure and hence, loss of fluorescence. Physiologically relevant forces are on the scale of a few pN. Destabilizing mutations may be necessary to access this force regime with GFP. Published in PNAS, 2004: [pdf] [Editor's Choice].


DNA-linked, switchable hydrogels and hydrogel structures.

Qdots trapping and release T Liedl, H Dietz, and FC Simmel.
Controlled trapping and release of nanoscale objects in a biological environment is of great significance for drug delivery and biosensing. Hydrogels have been studied extensively as drug delivery systems. Gel swelling and component release has been controlled mostly by temperature or pH changes and in a few cases by biologically relevant molecules such as saccharides or antigens. We explored the potential of a DNA-switchable polyacrylamide hydrogel to trap and release fluorescent quantum dots as model drug delivery vehicles. Trapping is achieved by the addition of DNA crosslinker molecules to a hybrid polyacrylamide DNA solution. Release of the particles from confinement is triggered by addition of a DNA release sequence. Single particle fluorescence microscopy is applied to study the mobility of individual nanoparticles. The kymographs on the left document trajectories of individual particles in the gel (A: free diffusive, B: trapped, C: release triggered). This system might form the basis of an intelligent delivery system, able to respond to DNA or RNA stimuli (such as mRNA active gene indicators). Published in Small, 2007: [pdf].

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