Over the course of this project, we have developed and implemented a new AI-supported de novo protein design pipeline (Frank et al., Science 2024), which makes it possible to construct unpredecently large custom proteins with high design accuracy. We expect this approach to enable combining de novo protein design with DNA nanotechnology to leverage the distinct strengths of both molecular frameworks. DNA origami contributes a rigid, programmable scaffold, while designed proteins introduce highly specific binding sites, enzymatic functions, or increased thermal stability. By precisely positioning these proteins on DNA scaffolds, we may achieve multivalent interactions with cells and can selectively incorporate catalytic modules. This synergy has the potential to enable co-delivery of DNA and protein therapeutics in a single carrier, outclassing conventional single-platform systems in robustness and versatility.
Prior work predominantly focused on either DNA- or protein-based carriers, but the project’s integration of pH-responsive DNA motifs with sophisticated membrane fusion strategies and fully customized protein scaffolds offers an unprecedented degree of control over target recognition, cargo release, and intracellular trafficking. The high efficiency of nuclear import observed in arrested cells (Liedl et al., JACS 2023) was an unanticipated outcome, indicating new opportunities for transfection in otherwise challenging cell populations. Another noteworthy surprise involved the rapid kinetics of membrane budding enabled by cholesterol-modified origami shells (Pinner et al., under review). Experimental data show that geometry-optimized DNA assemblies can efficiently drive membrane remodeling. Until the end of the project we expect to make significant strides toward improving bottleneck steps such as endosomal escape and trafficking to the nucleus.
Overall, these findings extend well beyond previous achievements in gene delivery, membrane engineering, and synthetic biology. Going forward, the project’s hybrid design paradigm, uniting protein functionalities with carefully assembled DNA architectures, will provide a powerful new toolbox for targeted delivery and triggered release but also sheds light on fundamental processes like membrane remodeling and nuclear transport. In doing so, it opens up new possibilities for precisely engineered therapeutic vehicles that surpass the limitations of earlier generation platforms, setting a precedent for advanced cellular applications.
