What's Your Availability? Novel Substrate Design for DNA Catalytic Reaction Networks Based on Thermodynamic Analysis of Target Molecules


Daniel Kelly

Document Type

Student Presentation

Presentation Date

April 2016

Faculty Sponsor

Elton Graugnard


Lung cancer is the leading cause of cancer deaths largely due to the lack of early detection. The most common lung cancer is non-small cell lung carcinoma (NSCLC), and the presence of NSCLC cells has been linked to altered expression levels of specific micro-RNAs (miRNAs) found in the blood stream. These cancer-specific miRNA expression profiles can be detected using reverse-transcription polymerase chain reaction (RT-PCR), yet this technique has not become a widely used method for clinical diagnosis. As an alternative to RT-PCR, DNA nanotechnology may provide clinical tools for detection of miRNA and disease diagnosis. Due to its programmable nature via Watson-Crick base pairing, DNA reaction networks can be constructed to detect low concentrations of complimentary target molecules (DNA or RNA) in solution. Detection begins when a target molecule hybridizes with a single stranded region (toehold) of a DNA reaction network component (substrate). However, the target molecules exhibit specific secondary structures (internal base pairing), which affects their interaction with the substrate and reduces network performance. The hypothesis of my research is that toehold location within the substrate can be optimized through thermodynamic analysis of the target molecule’s secondary structures. Here, we report preliminary results for optimized toehold placement in catalytic DNA reaction networks for detection of NSCLC-specific miRNA.

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