Protein-based polymers that bond to DNA : design of virus-like particles and supramolecular nanostructures

<p> In this thesis it is demonstrated that it is possible to use Protein-based Polymers (PbPs) as synthetic binders of DNA (or any other negatively charged polyelectrolyte). The PbPs co-assemble with their DNA templates to form highly organized virus-like particles and supramolecular structures. A range of PbPs have been developed over the last decades that can be used as precision functional polymers, and which integrate the unique properties of both proteins and polymers. Many PbPs are based on nature-inspired simple repetitive amino acid sequences. In this thesis, different kinds of such sequences have been combined into PbPs that mimic complex natural functionalities. Being intermediate between proteins and polymers, it has been able to mimic complex functionalities typically found for folded proteins, while retaining the tunability and ease of control that is more characteristic for (synthetic) polymers. Indeed, using clear design rules, biosynthetic PbPs sequences have been obtained and produced that co-assemble with nucleic acids to form true artificial viruses, which mimic their natural counterparts in many respects.</p> <p> The motivation for developing artificial viruses derives among others from the growing interest in exploiting natural self-assembled virus structures to develop nanostructured materials. In addition, natural viruses are being used as scaffolds for delivering DNA in the context of gene therapy, to serve as vaccines (by displaying antigens), to template diverse materials, to produce energy, to catch light, to catalyze reactions, to serve as contrasting agents, etc. Developing artificial viruses would serve not only to advance our capabilities to understand and control the co-assembly of nanostructures, but would also generate useful synthetic biomaterials that are even more suited than natural viruses to be used as building blocks for nanostructured materials. In short, the successful development of artificial viruses may be expected to give rise not only to new insights on templated self-assembly, but will also be very important for a range of applications.</p> <p> The main part of the thesis is divided into three parts. In part I, “Complexation of DNA into virus-like particles”, we describe details of the molecular biomimetic strategy to design and produce PbPs with functionalities that mimic those of natural viruses. Part II, “Applications of protein-DNA complexes”, deals with the development of diblock PbP that coat DNA, and with their applications in gene delivery and optical mapping of long DNA. Finally, in part III: “Supramolecular nanostructures beyond DNA” we consider the co-assembly of our PbPs with templates other than DNA, and also consider their self-assembly in the absence of DNA.