Various protein-based organelles exist in nature that are involved in a wide variety of different metabolic pathways. However, the exact benefit and function of protein-based organelles is still not completely understood. In the first part of this thesis, we create virus-based nanoreactors to mimic these organelles and to gain more understanding about the benefits of performing reactions inside a protein capsid. These nanoreactors are made by encapsulating various different enzymes in the protein capsid of the cowpea chlorotic mottle virus (CCMV). Furthermore, we investigated their potential use for medical applications by studying their extracellular and intracellular interaction with cancer cells. To improve on the current design, it is important to understand both the assembly of the virus(-like) particles and their cellular interaction. Therefore, in the second part of this thesis we aim to understand the assembly processes of a virus protein capsid and to find the optimal shape for virus-based nanostructures for cellular uptake. Here the assembly of the capsid proteins of CCMV around various lengths and forms of DNA is studied, which resulted in the formation of various virus-based nanostructures with different (new) geometries. These structures are used to study the shape depended cellular uptake and fate in in different cell lines. The results presented in this thesis form a solid basis for further research in the use of CCMV for medical and other applications. The found benefits of the virus-based nanoreactors and nanostructures will hopefully lead to the development of new drug formulations. Thus viruses will not only make us ill, but eventually make us better instead.