Nanobiotechnology is a rapidly growing and extremely fascinating field that, in one aspect, aims to rationally and selectively design biological molecules to perform advanced functions (the other aspect is to design non-biological platforms for biological processes). The most common biological molecules used are DNA, RNA and proteins for the reason that they may be conveniently and reliably produced by a variety of processes (PCR, IVT, IVTT, solid-state synthesis, etc). A few days ago I even mentioned one of these methods, DNA nanostructures (sometimes called DNA origami) and the amazing things they can do with biological computing. While there hasn’t been a world-changing breakthrough in the application of these structures yet, there has been some really interesting possibilities demonstrated. One of my favorites comes out of the institute I’m getting my PhD at and describes the application of DNA nanostructures as a platform for the directed assembly of synthetic vaccines.
Fortunately, the field is rich in brilliant scientists thinking of ways to push the boundaries.
In a April 28, 2013 Chemical Biology paper a collaborative group of researchers in Slovenia and UCSF describe the rational design, production and characterization of a three-dimensional nanostructure folded out of a single peptide chain. What is most interesting is that this group strayed from the traditional path of peptide-based structure design. Normally, structural peptide design has been based on motifs and structures which are commonly found in natural proteins. De novo fold design and synthesis has been unsuccessful with the exception of a few cases.
The current report describes the application of a platform wherein interacting coiled-coil motifs drove the self-assembly of the protein fold. In this way, the group was able to design a tetrahedral structure which was very unlike protein folds found in nature. They went further and visually characterized their protein using AFM to directly see the small, three-dimensional, pyramid-like shapes. Additionally, they demonstrated the ability to functionalize these structures by attaching split pieces of the fluorescent protein YFP to different vertices of the tetrahedron (shown above). One during proper folding would the YFP assembly correctly and show fluorescence. When the folding of the structure was disrupted, or if a position was deleted, the structure would align the segments of YFP and no fluorescence was be observed. While, this is a type of experiment which has been performed in other studies (i.e., the assembly of a Malachite Green RNA aptamer in RNA-based nanocube structures), it is an elegant and promising example of rationally designing peptide-based, non-natural structures.
The authors discuss the possibility of using these design principles for making nanostructures with cavities for drug delivery or for orienting synthetic catalytic sites. I’m excited to see what will come from subsequent studies, and also to see which biomolecule will be crowned king of the nanobiotech field – DNA? RNA? Protein?
1. Gradišar, H. et al. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nature chemical biology 1–6 (2013).doi:doi:10.1038/nchembio.1248