pH-Based immunoassay: explosive generation of hydrogen ions through an immuno-triggered nucleic acid exponential amplification reaction.

In this work, we propose a novel concept and a proof-of-concept strategy for the fabrication of a pH-based immunoassay platform with a certain degree of universality and scalability to make it adaptable for different application scenarios. The immunoreactions for the target detection are converted to pH changes through an engineered and optimized isothermal nucleic acid amplification, named exponential amplification reaction (EXPAR). Thus, a variety of well-developed methods for pH analysis, e.g. pH indicators, pH-strips and pH meters, can be applied for immunoassay directly. Here, we show that this proof-of-concept strategy is applicable for both macromolecular and micromolecular antigens by adopting human platelet-derived growth factor-BB (PDGF-BB) and chloramphenicol (CAP) as the model targets, respectively. The detection can be achieved using a colorimetric pH indicator after a 15 min reaction of the immuno-triggered isothermal nucleic acid amplification. In addition, compared with the traditional enzyme-linked immunosorbent assay (ELISA), the performance of our strategy, especially the detection limits, is improved to varying degrees for different targets, making the strategy a promising alternative for diverse application scenarios of immunoassay.

A nanoflow cytometric strategy for sensitive ctDNA detection via magnetic separation and DNA self-assembly.

Circulating tumor DNA (ctDNA) is a tumor-derived fragmented DNA in the bloodstream that is not associated with cells. It has been greatly focused in the recent decade because of its potential clinical utility for liquid biopsies. Development of ctDNA analytical techniques with high sensitivity and cost-efficiency will undoubtedly promote the clinical spread of ctDNA testing. In this paper, we propose a novel flow cytometry-based ctDNA sensing strategy which combines enzyme-free amplification and magnetic separation. The target DNA is capable of triggering a hybridization chain reaction, producing a fluorescent long linear assembly of DNA, which can be further captured by magnetic beads to present fluorescent signals using flow cytometry. In comparison with some conventional methods, our strategy has the advantages of easy operation and cost-efficiency, and thereby shows a promising application in clinical diagnosis. Graphical abstract.

Target-independent hybridization chain reaction-fluorescence resonance energy transfer for sensitive assay of ctDNA based on Cas12a.

Circulating tumor DNA (ctDNA) is a noninvasive biomarker which offer valuable information for cancer diagnosis and prognosis. In this study, a target-independent fluorescent signal system, Hybridization chain reaction-Fluorescence resonance energy transfer (HCR-FRET) system, is designed and optimized. Combined with CRISPR/Cas12a system, a fluorescent biosensing protocol was developed for sensing assay of T790 M. When the target is absent, the initiator remains intact, opens the fuel hairpins and triggers the following HCR-FRET. At presence of the target, the Cas12a/crRNA binary complex specifically recognizes the target, and the Cas12a trans-cleavage activity is activated. As a result, the initiator is cleaved and subsequent HCR responses and FRET processes are attenuated. This method showed detection range from 1 pM to 400 pM with a detection limit of 316 fM. The target independent property of the HCR-FRET system endows this protocol a promising potential to transplant to the assay of other DNA target in parallel.

A toehold-mediated strand displacement cascade-based DNA assay method via flow cytometry and magnetic separation.

Sensitive assay of EGFR T790M, a circulating tumor DNA marker in non-small-cell carcinoma, provides critical information for the decision of clinical treatments, evaluation of radiotherapy effect, and monitoring the progress of recurrence and metastasis. In this report, a novel flow cytometry-based sensing method is proposed for detecting T790M. The toehold-sequence hybridizes with the biotin-labeled initiator sequence and forms IT-dsDNA. The presence of a target induces the displacement of initiator-sequence from IT-dsDNA. The targets are continuously set free with the aid of a helper hairpin sequence for the next cycle. In tandem, the free initiator sequence starts the hybridization chain reaction, which binds the serial of fluorescence-labeled probe sequences. The products of the hybridization chain reaction are captured and separated by magnetic beads, which are finally assayed via flow cytometry. The capability to distinguish single-nucleotide polymorphism and the tolerance of complex matrix in blood serum indicate that this strategy has the promising potential to be applied in the liquid biopsy of clinical samples.