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Engineering high-performance hairpin stacking circuits for logic gate operation and highly sensitive biosensing assay of microRNA

Abstract

Recently, hairpin stacking circuits (HSC) based on toehold-mediated strand displacement have been engineered to detect nucleic acid and protein. However, the three metastable hairpins in HSC system can potentially react non-specifically in the absence of the catalyst, limiting its practical application. Here, we developed a unique hairpins design guideline to eliminate circuit leakages of HSC, and the high-performance HSC was successfully implemented on logic gates building and biosensing. We began by analyzing the sources of circuit leakages and optimizing the toehold length of hairpins in the HSC system based on surface plasmon resonance (SPR) technique. Next, a novel strategy of substituting two nucleotides in a specific domain, termed ‘loop-domain substitution’, was introduced to eliminate leakages. We also systematically altered position and number of the introduced substitutions to probe the potential contribution to circuit leakage suppression. Through these efforts, the circuit leakage of HSC was significantly reduced. Finally, by designing different DNA input strands, the logic gates could be activated to achieve the output signal. Using miRNA as model analyte, this strategy could detect miRNA down to pM levels with minimized circuit leakage. We believe these work are significant progresses in DNA circuitry.

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Publication details

The article was received on 01 Oct 2017, accepted on 03 Nov 2017 and first published on 06 Nov 2017


Article type: Paper
DOI: 10.1039/C7AN01624G
Citation: Analyst, 2017, Accepted Manuscript
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    Engineering high-performance hairpin stacking circuits for logic gate operation and highly sensitive biosensing assay of microRNA

    Y. Xing, X. Li, T. Yuan, W. Cheng, D. Li, T. Yu, X. Ding and S. Ding, Analyst, 2017, Accepted Manuscript , DOI: 10.1039/C7AN01624G

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