The overall aim of this thesis is to investigate the combination of supramolecular cylinders with DNA nanotechnology and assess any effects that can occur through binding and any applications this could have in biomedical therapy applications. From this base it is hoped that insight can be gained as to whether supramolecular chemistry can be used to create DNA nano-machines, capable of triggered release of cargo. The thesis begins with a review of DNA discovery, structure and binding by small molecules, followed by a review of the field of DNA nanotechnology. By expanding on the field of DNA nanotechnology recognition, chapters 2 and 3 will highlight the advantages of supramolecular chemistry when combined with DNA nanotechnology in both nano-machines and inside cell systems with a focus on DNA tetrahedral nanostructures. Chapter 4 researches the photocleavage capabilities of a ruthenium cylinder and the possibilities of selective release and photodynamic therapy using a DNA tetrahedron. Chapter 5 illustrates a new class of anti-viral agents capable of structure recognition regardless of RNA sequence. The chapter focuses on the inhibition of binding between the TAR RNA and ADP-1 peptide found in the HIV-1 virus.