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Designing Hybridization Chain Reaction Monomers for Robust Signal Amplification

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Engineering a Robust DNA Circuit for the Direct Detection of Biomolecular Interactions

Part of the book series: Springer Theses ((Springer Theses))

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Abstract

Methods to amplify the signal of biomolecular recognition events are essential for the detection of low target count encountered in applications such as early disease diagnosis. Hybridization chain reaction (HCR) is an attractive isothermal, enzyme-free amplification scheme involving the localised hybridization of metastable DNA hairpins into one-dimensional DNA assembly. One challenge in HCR is the difficulty in converting the molecular assembly event into a turn-on optical signal in a one-pot format which limits its utility as a general signal amplification tool. In this work, we established a four-point hairpin guidelines for the design of hairpin sequences through simulations and experimental validation. This enabled greater flexibility to customise specific hairpin sequences for use with the readout platform of interest. Using a shorter hairpin stem length, a one-pot signal amplification system was demonstrated by incorporating distance-sensitive Förster resonance energy transfer (FRET) readout. Controlled amplification was achieved as characterized by the predictable relationship between the detection dynamic range and hairpin concentration. We anticipate this HCR FRET system to be useful for the in situ detection and localized visualization of biological events.

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Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore

    Dr. Ang Yan Shan

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  1. Dr. Ang Yan Shan
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Yan Shan, A. (2018). Designing Hybridization Chain Reaction Monomers for Robust Signal Amplification. In: Engineering a Robust DNA Circuit for the Direct Detection of Biomolecular Interactions. Springer Theses. Springer, Singapore. https://doi.org/10.1007/978-981-13-2188-7_5

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