Abstract
Isothermal, enzyme-free amplification methods based on DNA strand-displacement reactions show great promise for applications in biosensing and disease diagnostics but operating such systems within biological environments remains extremely challenging due to the susceptibility of DNA to nuclease degradation. Here, we report a catalytic hairpin assembly (CHA) circuit constructed from nuclease-resistant l-DNA that is capable of unimpeded signal amplification in the presence of 10% fetal bovine serum (FBS). The superior biostability of the l-DNA CHA circuit relative to its native d-DNA counterpart was clearly demonstrated through a direct comparison of the two systems (d versus l) under various conditions. Importantly, we show that the l-CHA circuit can be sequence-specifically interfaced with an endogenous d-nucleic acid biomarker via an achiral peptide nucleic acid (PNA) intermediary, enabling catalytic detection of the target in FBS. Overall, this work establishes a blueprint for the detection of low-abundance nucleic acids in harsh biological environments and provides further impetus for the construction of DNA nanotechnology using l-oligonucleotides.
Highlights
The straightforward programmability of Watson–Crick (WC) base pairing interactions makes nucleic acids an ideal material for engineering nanoscale structures and devices
It is not surprising that significant effort has gone into engineering non-enzymatic DNA amplifier circuits that can detect and amplify nucleic acid signals based on strand-displacement mechanisms [15]
Our goal was to design a catalytic hairpin assembly (CHA) circuit comprised of l-DNA that could be interfaced with disease-relevant nucleic acid biomarkers
Summary
The straightforward programmability of Watson–Crick (WC) base pairing interactions makes nucleic acids an ideal material for engineering nanoscale structures and devices. DNA strand-displacement reactions have been widely used for engineering molecular devices, including motors and walkers [4,5,6,7], reconfigurable DNA nanostructures [8,9], and logic circuits [10,11,12]. Such devices can be interfaced with regulatory nucleic acids (e.g., mRNAs and microRNAs) via WC base pairing [13,14], making them well suited for applications in bioengineering and disease diagnosis. Examples of DNA amplifiers include entropy driven catalytic circuits [16], hybridization chain reactions [17] and various
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