Design of DNA Monomers as an Amplification Toolbox

The ability to amplify signals from biomolecular recognition events is highly sought after, particularly for detecting low target count. Hybridization chain reaction (HCR) is an attractive enzyme-free method based on the programmed self-assembly of solely DNA hairpin monomers upon activation by a complementary trigger. In this work, we established an explicit set of four-point design guidelines on the lengths and CG content of the hairpin toehold and stem domains. This provides a rational approach towards HCR hairpin design, as compared to the usual trial-and-error process. The guidelines were used to design hairpins of shorter stem length, which improved the hairpin opening kinetics and facilitated the incorporation of a distance-sensitive FRET readout. The HCR FRET system remained robust against circuit leakage in diverse buffer environments, temperature and biological interferences. This is an important step forward in providing the flexibility to re-design HCR hairpins for various signal amplification applications.


Yung Large


This work has been published in Chem Comm on Feb 16, 2016 (doi: 10.1039/C5CC08907G)

Corresponding author(s): Lanry Yung Lin-Yue ( This email address is being protected from spambots. You need JavaScript enabled to view it. )
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