Polyvalent Oligonucleotide Gold Nanoparticle Conjugates: Versatile Nanostructures for Biodetection and Chemically Programmable AssemblyPublic Deposited
Polyvalent oligonucleotide functionalized gold nanoparticle conjugates (DNA-AuNPs) possess unusual properties, which derive from their particle and oligonucleotide subunits as well as their three-dimensional architectures. This dissertation explores the role each chemical component plays in the conjugate's architecture and assembly and recognition capabilities. It also describes their application as probes in novel biodetection assays. In chapter two, the relationship between AuNP radius of curvature and oligonucleotide packing is investigated. Mathematic relationships are developed, which can predict oligonucleotide loading on anisotropic gold nanomaterials. Additionally, as the AuNPs approach 100 nm in diameter, their loading capacities begin to mimic that of a macroscopically flat surface. In chapter three, the ability of DNA bases to frame shift or 'slip' when attached to a curved gold nanoparticle surface is shown. This suggests that nucleotide bases, when attached to gold nanoparticles, adapt to form the strongest hybridization arrangements available to them based on their local geometry. This contributes to the increased melting temperature observed for hybridized DNA-AuNPs as compared to free duplex DNA. Consistent with this conclusion, slipping interactions are not observed with DNA-functionalized flat gold nanoprisms. In chapter four, the role duplex DNA plays in modulating the unit cell parameters of highly ordered face-centered-cubic crystal lattices of DNA-AuNPs is investigated. Nanoparticle spacing increases linearly with DNA length, yielding maximum unit cell parameters of 77 nm and 0.52 % inorganic-filled space. In chapter five, the development of a novel oligo-AuNP probe that can be used in the bio-barcode assay is reported. This quantitative assay relies on chemical liberation of adsorbed thiolated oligonucleotides from AuNP surfaces with dithiothreitol yielding a 7 aM assay limit of detection. In chapter six, a way of using the bar code assay to detect bacterial genomic DNA is reported. A critical step in the assay involves the use of blocking oligonucleotides which bind to specific regions of the target DNA and prevent the strands from re-hybridizing, thus allowing the particle probes to bind. The limit of detection for this assay was 2.5 fM, and the development of the assay represents an important step towards non-enzymatic detection of genomic DNA.