Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor

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dc.contributor.advisorChen, Jennifer I-Ling
dc.contributor.authorGhotra, Gurbrinder
dc.date.accessioned2020-11-13T13:42:32Z
dc.date.available2020-11-13T13:42:32Z
dc.date.copyright2019-03
dc.date.issued2020-11-13
dc.date.updated2020-11-13T13:42:32Z
dc.degree.disciplineChemistry
dc.degree.levelMaster's
dc.degree.nameMSc - Master of Science
dc.description.abstractWe present a method for modulating the kinetics and thermodynamic properties of aggregation and disassembly processes of DNA-functionalized nanoparticles. Specifically, we examine factors influencing the toehold strand-displacement reaction on nanoparticle surfaces. Gold nanoparticles were functionalized with oligonucleotide sequences with varying surface density by incorporating diluent DNA strands. The hybridization of DNA yields aggregates which then disassemble via a strand-displacement reaction by the target sequence. Localized surface plasmon resonance of gold nanoparticles and fluorescently tagged DNA strands were employed to gain an understanding of the aggregation and disassembly steps. The surface density of DNA impacts the aggregation kinetics, the melting temperature and the target-induced disassembly of these nanoaggregates. It does so by modulating the cooperativity and attinebility of the oligonucleotides, the electrostatic repulsion between the nanoparticles and the accessibility of the linkers to the target nucleic acid. A dramatic decrease in the initiation time and increase in the rate of disassembly are achieved by optimizing the surface density. Our work provides insight into the strand-displacement reaction on nanoparticle surfaces that underpins various sensing and DNA-driven nanomachine applications. This fundamental understanding allowed the design of a label-free, low cost and miniaturized biosensing platform based on the disassembly of core-satellite nanoassemblies. We successfully manipulate the system for the rapid and selective detection of a nucleic acid biomarker microRNA-210, enabling diverse biological applicability
dc.identifier.urihttp://hdl.handle.net/10315/37851
dc.languageen
dc.rightsAuthor owns copyright, except where explicitly noted. Please contact the author directly with licensing requests.
dc.subjectMaterials Science
dc.subject.keywordsLocalized surface plasmon resonance
dc.subject.keywordsPlasmonic nanoparticles
dc.subject.keywordsBiosensor
dc.subject.keywordsmiRNA detection
dc.subject.keywordsAttinebility
dc.subject.keywordsDNA functionalized Gold nanoparticle
dc.subject.keywordsOligonucleotide
dc.subject.keywordsDNA surface density
dc.subject.keywordsToehold-mediated strand displacement reaction
dc.subject.keywordsFRET
dc.subject.keywordsAggregation
dc.subject.keywordsDisassembly
dc.subject.keywordsDarkfield microscopy
dc.subject.keywordsCooperativity
dc.subject.keywordsAvidity
dc.subject.keywordsLabel-free
dc.subject.keywordsLow cost
dc.subject.keywordsMiniaturized
dc.subject.keywordsBiosensing
dc.subject.keywordsCore-satellite nanoassemblies
dc.subject.keywordsAffinity
dc.subject.keywordsDNA hybridization
dc.subject.keywordsPlasmonic coupling
dc.subject.keywordsCalorimetric assay
dc.subject.keywordsDNA crowding
dc.subject.keywordsPoint-of-care
dc.subject.keywordsHypoxia
dc.subject.keywordsNormoxia
dc.subject.keywordsDirect detection
dc.titleOptimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor
dc.typeElectronic Thesis or Dissertation

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