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dc.contributor.advisorYin, Peng
dc.contributor.authorXu, Weidong
dc.date.accessioned2020-10-16T14:56:50Z
dash.embargo.terms2022-05-01
dc.date.created2020-05
dc.date.issued2020-05-11
dc.date.submitted2020
dc.identifier.citationXu, Weidong. 2020. Super-Resolution Geometric Barcoding With Programmable Self-Assembly and Programmable Autonomous Blinking. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences.
dc.identifier.urihttps://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37365991*
dc.description.abstractGeometric barcoding has shown promise in fluorescence imaging applications for multiplexed, specific and sensitive detection of single molecules. This dissertation presents a super-resolution geometric barcoding scheme, which combines the advantages of DNA nanotechnology and super-resolution imaging. First, I presented a DNA nanostructure based geometric barcoding scheme compatible with super-resolution imaging with DNA-PAINT (Point Accumulation for Imaging in Nanoscale Topography), which enabled the capture and visualization of multiple distinct molecular targets inside each individual DNA nanostructure. I summarized the design principle and technical considerations of our geometric barcoding platform, and demonstrated 2 strategies for increasing the multiplexing capability of our geometric barcoding system. Next, I applied this super-resolution geometric barcoding system to multiplexed miRNA profiling. We used synthetic DNA nanostructures as programmable miRNA capture "nano-array", and visualized our geometric barcoding platform with captured miRNAs by applying DNA-PAINT method. We demonstrated high-specificity (single nucleotide mismatch discrimination), multiplexed (8-plex, 2 panels) and sensitive measurements on synthetic miRNA samples, and applied one 8-plex panel to measure endogenous miRNAs levels in total RNA extract from HeLa cells. Finally, I developed a MATLAB DNA-PAINT data analysis software package based on an earlier version, as an effort to improve the accessibility and reproducibility of DNA-PAINT method and technologies based on it, including our super-resolution geometric barcoding platform. I summarized the key features that we implemented for DNA-PAINT data processing and data quality assurance, including their principle and usage, and discussed the architecture design choices and the future development of the software.
dc.description.sponsorshipChemistry and Chemical Biology
dc.format.mimetypeapplication/pdf
dc.language.isoen
dash.licenseLAA
dc.subjectDNA nanotechnology
dc.subjectDNA-PAINT
dc.subjectmicroRNA
dc.subjectmultiplexing
dc.subjectsuper-resolution imaging
dc.subjectgeometric barcoding
dc.subjectsoftware development
dc.titleSuper-Resolution Geometric Barcoding With Programmable Self-Assembly and Programmable Autonomous Blinking
dc.typeThesis or Dissertation
dash.depositing.authorXu, Weidong
dash.embargo.until2022-05-01
dc.date.available2020-10-16T14:56:50Z
thesis.degree.date2020
thesis.degree.grantorGraduate School of Arts & Sciences
thesis.degree.grantorGraduate School of Arts & Sciences
thesis.degree.levelDoctoral
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy
thesis.degree.nameDoctor of Philosophy
dc.contributor.committeeMemberSzostak, Jack
dc.contributor.committeeMemberShih, William
dc.type.materialtext
thesis.degree.departmentChemistry and Chemical Biology
thesis.degree.departmentChemistry and Chemical Biology
dash.identifier.vireo
dc.identifier.orcid0000-0002-9457-1036
dash.author.emailxuwd11@gmail.com


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