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SINGLE-MOLECULE IMAGING OF DNA ON GOLD NANOPARTICLE SURFACES
Bender, Abigail Paige Crawford
Bender, Abigail Paige Crawford
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Thesis/Dissertation
Date
2024-12
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Chemistry
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https://doi.org/10.34944/karx-ma15
Abstract
Deoxyribonucleic acid (DNA) is a popular receptor material for biosensors in applications such as medical diagnostics, environmental monitoring, and food safety. Many of these sensors rely on the hybridization of DNA, either to a target nucleic acid or to itself, in order to produce a measurable signal. One way to increase the sensitivity and tunability of DNA-based biosensors is by tethering the strands to a nanoparticle surface, although questions remain about how DNA melting behavior changes when confined to a surface and the implications these effects could have on biosensor performance. In this work, we use single-molecule fluorescence imaging to explore the thermodynamics of DNA melting on gold nanoparticle surfaces. We first discuss the development of a nanothermometry technique based on a super-resolution imaging technique called DNA-PAINT that allows us to indirectly study the local temperature of DNA-functionalized gold nanoparticle arrays. This method is non-perturbative to the system and allows us to probe the hybridization status of DNA on a single-strand basis, providing spatial information that enables us to investigate the cooperative properties of surface-tethered DNA. In our second chapter, we use this technique to investigate how the thermodynamics of surface-tethered DNA melting are impacted by various aspects of the melting environment. We found that DNA on surfaces exhibits anomalous salt-dependent melting behavior when compared to solution-phase studies. By analyzing both the melting temperature and melting transition width, we can see how the behavior is affected by the DNA length, ion concentration and identity, and distance between the DNA and the nanoparticle surface.
Finally, we think about the implications of these findings on DNA-nanoparticle biosensors and explore what aspects still need further investigation, including the potential of super-resolution reconstructions to help us understand DNA cooperativity. Overall, the work in this dissertation highlights the differences between surface-tethered and solution-phase DNA behavior and the need to understand the various influential factors within DNA monolayers for successful biosensor design.
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