Programmable Hybridization Assemble Nicked Displacement Amplification for Detecting Ricin Toxin

Abstract Isothermal amplification, such as hybridization chain reaction (HCR), is a simple and reliable method for detecting signal amplification. However, the hairpin in HCR will not fully participate in the reaction. And after the hairpin is opened, the distance between the fluorophore and the quencher does not change much. Therefore, the signal magnification is limited. Here, we designed a new isothermal amplification method named hybridization assemble nicked displacement amplification (HANDA), combining HCR and strand displacement amplification (SDA) ingeniously. HANDA first triggers HCR through the target sequence to form long double-strand DNA (dsDNA) with gaps. Then SDA is performed from the gap to obtain a large amount of single-stranded DNA (ssDNA), so as to achieve the purpose of double signal amplification. The base sequence of DNA hairpin had also been optimized. The best sequence design rule was found and had universal applicability. We have demonstrated that HANDA combined with DNA barcodes can be used for trace detection of ricin. This new isothermal amplification method provides an effective and universal platform for the trace detection of various toxic substances.