DNA Templated Self-Assembly

Abstract

This thesis has been concerned with DNA templated self-assembly, with the long term goal to create well-defined nano-architectures based on p-conjugated molecules. Before realizing this goal, single-stranded DNA has been investigated to see if it can be used as a template to bind organic guests, such as p-conjugated molecules, via hydrogen (H) bonding. Furthermore, experimental techniques and theoretical models have been used to characterize these DNA templated assemblies and to determine how the guests are distributed on the templates. In Chapter 2, oligothymine templates of different length have been used to organize naphthalene based small molecules having a complementary diaminotriazine H bonding unit, to create monodisperse assemblies in which the length is defined by the template. The structure of these hybrid assemblies has been characterized in detail by a combined experimental and theoretical study. These experiments have revealed that the DNA templated self-assemblies have a right-handed helical arrangement and are held together by p-p, hydrophobic, and H bond interactions. Through the use of a theoretical mass-action model for the templated selfassembly, the host-guest and guest-guest interaction energies have been estimated by fitting the spectroscopic data. A qualitative theoretical picture of the way in which the guests are physically distributed on the templates has been obtained. Short templates are filled one-by-one at moderate fractions of bound sites. For larger templates first alternating sequences of filled and empty sections appear, before at larger fractions of bound sites, virtually all of the binding sites for all template lengths are filled. In Chapter 3, the binding of p-conjugated oligomers with DNA has been explored as a first step towards the construction of well-defined stacks in which the position of the p– conjugated molecules is directed by the DNA template via H bonding. These studies have revealed that large p-conjugated molecules in water have a strong tendency to self-assembly in a nontemplated fashion, which limits their application for DNA templated self-assembly. Increased guest–guest interaction energy between guests on the template can change the supramolecular organization of the templated self-assembly and can induce further aggregation into assemblies larger than the size of the template. Peptide nucleic acids have also been used as a template for the self-assembly of p-conjugated molecules in organic solvents. Here, the nontemplated self-assembly can be suppressed, yielding PNA templated self-assemblies of a discrete size. In Chapter 4, the use of electrospray ionization mass spectroscopy to characterize the DNA templated self-assemblies has been investigated. The highest complex mass detected is 15 kDa: a 20 component self-assembled object. Gas phase breakdown experiments on single and multiple guest–DNA assemblies have given qualitative information on the fragmentation pathway and the relative complex stability. The guest molecules are removed from the template one by one in a controlled way. The stabilities of the complexes depend mainly on the molecular weight of the guest molecules, suggesting that the complexes collapse in the gas phase. The use of oligomeric guest molecules to enhance the stability of the DNA templated assemblies have been explored in Chapter 5. The analyses performed on the DNA hybridization in this chapter have shown that binding guest strands with multiple binding sites stabilizes the complex significantly. Furthermore, it has been found that guest–guest interactions additionally stabilize the DNA hybridization of smaller oligomeric guest strands to a larger template strand. This concept has also been successfully applied to a synthetic guest molecule. In Chapter 6, a naphthalene based guest equipped with a diaminopurine H bonding unit is synthesized to enhance the stability of the DNA templated self-assemblies by increasing the guest–guest interaction. Temperature and concentration dependent UV–vis and circular dichroism data have shown that the guest–guest interaction is indeed improved, but unfortunately the host–guest interaction energy is slightly lower compared to the earlier reported oligothymine templated self-assemblies. These DNA templated self-assembly have also been studied at different pH values. Upon protonation of the guests the templated self-assembly undergoes a helix reversal which leads to an increased host–guest and guest–guest interaction energy.