UC San Diego

Quantifying the interactions between biomolecules combined with discovering their structure provides better understanding of the underlying molecular mechanisms and opens the capability to accurately predict and design micromolecular structures and interactions. The ability of this approach to advancing the diagnostics and the treatment of disease is immense. In this thesis, it was demonstrated that two resonant optical nanoprobes, namely photonic crystal microcavity sensor and plasmon-coupled nanoparticle probe can be applied toward investigating biomolecular interactions. Both techniques are based on the measurements of optical resonances. Measurement of protein binding kinetics using photonic crystal microcavity sensor was demonstrated for the first time. Real-time monitoring of the resonant wavelength provides information on the strength of protein binding and concentration. The sensor performance was demonstrated with biotinylated-BSA and anti-biotin. Mass transport of molecules to the sensing surface was analyzed to explain the relatively long transition time needed to reach the binding equilibrium in time resolved experiments. Binding of small molecular species such as aromatic rings was detected. The detection limit, in terms of the mass of molecules bound to the surface, was shown to be less than 4.5fg. The small modal volume and photonic confinement inside the microcavity enable detection of attoliter samples. The calculations show that the response of the sensor to binding of a single molecule is 0.72pm. By implementing temperature control and signal processing techniques, signal-to-noise ratio can be improved to allow for single molecule detection. Plasmon coupled- nanoparticle probes were used to measure the binding strength between two DNA strands, with the idea to discern single nucleotide mismatches in the sequence. The probe consists of two streptavidin-coated gold nanoparticles interconnected with two biotinylated-DNA strands under test. An external Coulombic force was applied by lowering the ionic concentration of the solution, causing the binding strength between complementary DNA strands to be weakened. This was converted to a distance change between plasmon-coupled gold nanoparticles, causing a shift in their resonant wavelength position. This is a new approach to the measurement of the binding strength within molecular complexes