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UBC Theses and Dissertations

Optimizing surface modifications for quantum dot self assembled monolayers (-via surface mediated DNA hybridization) on monocrystalline gold bead electrodes using electrochemistry coupled fluorescence imaging Sundar, Rochita


Surface hybridization of DNA strands on electrode surfaces (probes) with complementary DNA strands in solution (targets) forms the basis of several electrochemical biosensors used to detect nucleic acids of interest. This work aims to construct a site-selective assembly of probe strands on only some parts of the electrode surfaces to study specific and non-specific surface interactions of target strands during the hybridization step. The target strands used in this work have been precisely tailored onto a Quantum-dot (QD) surface. This ties to the larger goal of the project of assembling QDs on electrode surfaces. Such a surface has potential widespread bio-sensing application owing to QDs unique optical and surface properties. Monocrystalline gold bead electrodes displaying different surface features were coated in 11-Mercapto-1-undecanol solutions (or MUDOL). MUDOL was reductively removed by applying negative potentials only from some surface features of the electrodes. Subsequently, AF488 fluorophore tagged DNA strands were assembled onto these surface features either directly or following an assembly of 6-Meracpto-1-hexanol (or MCH) spacer molecules. The value of the applied negative potential, the DNA concentration used and time of electrode immersion in DNA solution were optimized to form low probe surface coverages and low probe surface densities. Preliminary hybridization experiments in the absence or presence of divalent Magnesium ions in the target solutions (containing either 0.2 DNA strands per QD, 2 DNA strands per QD or 10 DNA strands per QD bioconjugates) at room temperature or at an elevated temperature of 45°C were attempted. These surfaces were studied using a fluorescence microscope coupled with an electrochemical control. The results indicate that some of the targets interact with the surface probes non-specifically through weak van der Waals forces or may exist in a partially hybridized state. A small fraction of targets is able to hybridize (specifically interact) with the surface probes, and a still smaller fraction is stable at applications of negative potentials. It might be possible that the negative potentials induce electrochemical melting or dehybridization readily as the bulky nature of the QDs prevent a stable hybridized state.

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