Towards Minimally Interfering Reporting in DNA Reaction Networks


Kay Hadrick

Document Type

Student Presentation

Presentation Date

April 2016

Faculty Sponsor

Elton Graugnard, Natalya Hallstrom


The detection and quantification of disease-linked biomarkers could be an important tool for early diagnosis as well as in monitoring disease initiation and progression. These biomarkers occur in such low concentrations in the blood stream, however, that it is time-consuming and expensive to detect them. Recently, the fact that Watson Crick base-pairing can be programmed has enabled the development molecular non-enzymatic catalytic DNA based networks that can be used to detect, amplify, and report the presence of specific biomarkers. These DNA reaction networks typically consist of coupled catalytic circuits and DNA fluorescence resonance energy transfer (FRET) reporters. However, unintended reactions between the catalytic circuits and reporters can adversely affect network performance and reduce sensitivity. To simplify the network and eliminate the separate reporter, integrated TAMRA-TEX615 dye-dye pairs were incorporated directly into components of the catalytic circuit in order to study their impact on network performance. The preliminary results of our study show substantial changes in fluorescence intensity of these pairs with the addition of a catalyst to the circuit. These changes in fluorescence vary with excitation wavelength with the most dramatic change occurring at 560 nm for this particular pair. These preliminary results validate the feasibility of the integrated reporter approach as a path towards simplifying reaction network design and improving overall network performance.

This research was supported by the W.M. Keck Foundation, NIH Grant No. P20 RR016454 from the INBRE Program of the National Center for Research Resources, and The Micron Foundation. We also thank the Nanoscale Materials & Device Research Group (nano.boisestate.edu) for valuable assistance.

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