The aim of this work is to develop nanosized DNA cavities for proteins. Most of the DNA-scaffolded protein systems that make use of the DNA origami technology consist of enzyme cascades positioned on a DNA platform at a defined intermolecular distance. The majority of the studies reported so far in this field deal with the horse radish peroxidase and glucose oxidase pair, and only recently, more complex enzymatic reactions, like the transcription and processing of RNA within a DNA capsule, have been described. Along this line, the present work aims at developing a DNA-scaffolded translocation and protein unfolding device that can be employed as an up-stream module in multifunctional nano-fabrication devices.

In parallel, different strategies have been explored to extend the toolbox of available methods for protein attachment to DNA. Non-covalent and non-regioselective encapsulation of proteins into a DNA-scaffolded environments is currently of increasing interest as a potential aid in the structural elucidation of membrane bound proteins. In a similar fashion, we here investigate the encapsulation of proteins within DNA cavities using low affinity ligands for distinct amino acid groups distributed on the protein surface. In this way, the protein will be immobilized in various orientations within the DNA chamber, facilitating its structural elucidation and 3D model reconstruction.