Small Molecule-linked DNA Oligonucleotides for Target Protein Recognition and Inhibition
Oligonucleotides (ONs) are typically defined as short nucleic acid polymers that are 20 to 200 bases long. It has been well known that aptamers (single-stranded DNA or RNA ONs) can adopt distinct three-dimensional folded structures and bind to target proteins (or other target molecules) with high affinity and selectivity. While aptamers that target proteins represent a promising molecular recognition modality that exploits the self-folding nature of nucleic acids, alternative protein recognition elements, usually synthetic small molecules that are projected from an ON scaffold, can also be utilized for protein-binding purposes. In particular, ONs tethered to protein-binding small organic molecules have received recent attention due to the capability of synthetic molecules to serve as specific inhibitors of proteins associated with disease and so these synthetic moieties can complement or augment the molecular recognition capacity of ONs. Further, the ON domain can also (a) serve as a “barcode” to identify the synthetic fragments and (b) act as a scaffold to project them in a desired and programmable fashion. This dissertation starts with representative examples, wherein ONs serve as binding moieties and/or as projecting scaffolds for synthetic protein-recognition elements, discussed in chapter one, followed by the development of two novel ON-based protein inhibitors which further explore the approach of coupling synthetic protein-binding fragments with ON scaffolds. The first system, as described in chapter two, exhibits controllable protein inhibition against the target protein in selective response to a cancer-associated microRNA. The second system (explored in chapter three) features an aptamer core sequence flanked by small protein-binding elements. The resultant aptamer chimera is capable of forming a complex simultaneously with two target proteins, leading to dual inhibition.