Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is extensively used in healthcare for detection of genetic mutations and analysis of drug resistant pathogens. Here we developed a nucleic acid sensor able to differentiate between a fully matched analyte and one with a SNV in a wide temperature range of 5°C-32°C. The sensor, dubbed here the 'Owl Sensor' due to the complex's resemblance to owl eyes, utilizes recent developments in DNA nanotechnology and synthetic biology to self-assemble a fluorescent DNA nanostructure called a Double Crossover, or DX Tile, capable of differentiating SNVs in a large temperature range, including ambient temperature. In the presence of fully matched nucleic acid analytes, a stable complex is formed with high fluorescent signal; however in the presence of a single base variation in the analyte, unfavourable helicity results in little-to-no observed complex formation. The novelty of the approach is that selectivity of analyte recognition is, at least in part, determined by the structural rigidity of the entire nanostructure rather than by the stability of analyte-probe hybrid, as is the case for conventional hybridization probes. The rigid nanostructure collapses if a minor imperfection, e.g. if a single-base mispairing, is present. Owl Sensor differentiates fully matched analyte from mismatched in a wide temperature range, with mismatched analyte producing only the background fluorescence, selectivity that is hard to achieve by conventional hybridization probes. Owl Sensor therefore promises to add to the toolbox for diagnosis of genetic disorders and infectious diseases at ambient temperatures.
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Master of Science (M.S.)
College of Sciences
Length of Campus-only Access
Masters Thesis (Campus-only Access)
Karadeema, Rebekah, "The Owl Sensor: A Smart Nanostructure for Single Nucleotide Variation Analysis" (2016). Electronic Theses and Dissertations. 5467.