Final Report Summary - DNA ORIGAMI DEVICES (Single-molecule studies of protein-protein and protein-DNA interactions, enabled by DNA origami.)
The focus of the project was on exploiting the positioning capabilities of DNA origami for biophysical studies of the structure and dynamics of proteins and nucleic acids. Of particular interest were adhesive forces between biomolecules. To achieve our objectives, we first had to make DNA origami nanostructures available for practical applications, which required revising and augmenting the entire workflow for making DNA origami, and encompasses sequence design over raw-materials production and self-assembly of structures to purification.
Among other aspects, we have studied in detail how DNA origami objects form (Sobczak et al., Science 2012). Informed by our data, we developed new assembly protocols that can provide up to 100% synthesis yield in drastically reduced reaction times. We have added improved design rules (Martin et al, Nature Communications 2012), quality assays (Wagenbauer et al., Nature Communications 2014), preparation methods (Stahl et al., Angewandte Chemie, 2015), and scaled up the supply of materials (Praetorius et al., Nano Letters 2015). Also, DNA origami based nanofabrication has attracted interest particularly because of its potential to achieve atomic-scale positional control. In a high-resolution structural analysis study, we validated this assumption by producing a cryo electron microscopy 3D map of a discrete object (Bai et al., PNAS 2012) comprising ~15,000 DNA bases at user-defined coordinates in an object twice as big as a ribosome. In a high-resolution placement study, we used a DNA positioning device to tune the distance between molecules with atomic (Bohr radius) resolution (Funke et al., Nature Nanotech, 2015).
We have also developed the proposed DNA-origami biophysical nanotools, among them a synthetic DNA channel for lipid membranes (Langecker et al., Science 2012), which opens avenues for influencing the metabolism of cells. We have invented DNA-based 'gatekeepers' for single molecule kinetics with nanopore detectors (Wei et al., Angewandte Chemie 2012), and DNA-based 'grabbers' for the mechanical manipulation of single molecules with improved resolution (Pfitzner et al., Angewandte Chemie 2013). In two studies, currently in preparation for publication, we have dissected the stacking forces between DNA basepairs and resolved the distance-dependent interaction landscape for nucleosome assemblies, again using custom DNA nanotools. Recently, we have also developed a new method for making easily reconfigurable hierarchical assemblies from DNA, based on shape-complementary components that interact via weak contact interactions (Gerling et al., Science 2015). These methods enable us to create much more machine-like DNA nanostructures, as exemplified by a stochastic rotary apparatus (Ketterer et al., Science Advances, in the press) which we developed as a prototype platform for making active DNA motors in the future. Several other projects that we have started within the ERC starting grant ,such as a tethered-particle assay for studying receptor-ligand kinetics on the single-molecule level, will come to fruition soon.
Thanks to the financial possibilities as created by the ERC starting grant, the methods we have developed in my lab and the insights that we have obtained have helped take DNA origami from the proof-of-concept level to a widely applicable tool. Custom DNA origami may now be used to build nanoscale instruments to test biological and physical hypotheses. DNA origami may even have an industrial future.
Among other aspects, we have studied in detail how DNA origami objects form (Sobczak et al., Science 2012). Informed by our data, we developed new assembly protocols that can provide up to 100% synthesis yield in drastically reduced reaction times. We have added improved design rules (Martin et al, Nature Communications 2012), quality assays (Wagenbauer et al., Nature Communications 2014), preparation methods (Stahl et al., Angewandte Chemie, 2015), and scaled up the supply of materials (Praetorius et al., Nano Letters 2015). Also, DNA origami based nanofabrication has attracted interest particularly because of its potential to achieve atomic-scale positional control. In a high-resolution structural analysis study, we validated this assumption by producing a cryo electron microscopy 3D map of a discrete object (Bai et al., PNAS 2012) comprising ~15,000 DNA bases at user-defined coordinates in an object twice as big as a ribosome. In a high-resolution placement study, we used a DNA positioning device to tune the distance between molecules with atomic (Bohr radius) resolution (Funke et al., Nature Nanotech, 2015).
We have also developed the proposed DNA-origami biophysical nanotools, among them a synthetic DNA channel for lipid membranes (Langecker et al., Science 2012), which opens avenues for influencing the metabolism of cells. We have invented DNA-based 'gatekeepers' for single molecule kinetics with nanopore detectors (Wei et al., Angewandte Chemie 2012), and DNA-based 'grabbers' for the mechanical manipulation of single molecules with improved resolution (Pfitzner et al., Angewandte Chemie 2013). In two studies, currently in preparation for publication, we have dissected the stacking forces between DNA basepairs and resolved the distance-dependent interaction landscape for nucleosome assemblies, again using custom DNA nanotools. Recently, we have also developed a new method for making easily reconfigurable hierarchical assemblies from DNA, based on shape-complementary components that interact via weak contact interactions (Gerling et al., Science 2015). These methods enable us to create much more machine-like DNA nanostructures, as exemplified by a stochastic rotary apparatus (Ketterer et al., Science Advances, in the press) which we developed as a prototype platform for making active DNA motors in the future. Several other projects that we have started within the ERC starting grant ,such as a tethered-particle assay for studying receptor-ligand kinetics on the single-molecule level, will come to fruition soon.
Thanks to the financial possibilities as created by the ERC starting grant, the methods we have developed in my lab and the insights that we have obtained have helped take DNA origami from the proof-of-concept level to a widely applicable tool. Custom DNA origami may now be used to build nanoscale instruments to test biological and physical hypotheses. DNA origami may even have an industrial future.