Exonuclease III-assisted multiple cycle amplification for the sensitive detection of DNA with zero background signal

Sensitive and Specific Exonuclease III-Assisted Recombinase-Aided Amplification Colorimetric Assay for Rapid Detection of Nucleic Acids

The development of a contamination-free and on-site nucleic acid detection platform with high sensitivity and specificity but low-cost for the detection of pathogenic nucleic acids is critical for infectious disease diagnosis and surveillance. In this study, we combined the recombinase-aided amplification (RAA) with the exonuclease III (Exo III)-assisted signal amplification into a platform for sensitive and specific detection of nucleic acids of African swine fever virus (ASFV). We found that this platform enabled a naked eye visual detection of ASFV at a detection limit as low as 2 copies/μL in 30 min. As expected, no cross-reactivity was observed with other porcine viruses. In addition, to avoid aerosol contamination, a one-tube RAA-Exo III colorimetric assay was also established for the accurate detection of ASFV in clinical samples. Taken together, we developed a rapid, instrument-free, and low-cost Exo III-assisted RAA colorimetric-assay-based nucleic acid detection platform.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

Recent advances in biosensors for in vitro detection and in vivo imaging of DNA methylation

DNA methylation is the predominant epigenetic modification that participates in many fundamental cellular processes through posttranscriptional regulation of gene expression. Aberrant DNA methylation is closely associated with a variety of human diseases including cancers. Therefore, accurate and sensitive detection of DNA methylation may greatly facilitate the epigenetic biological researches and disease diagnosis. In recent years, a series of novel biosensors have been developed for highly sensitive detection of DNA methylation, but an overview of recent advances in biosensors for in vitro detection and especially live-cell imaging of DNA methylation is absent. In this review, we summarize the emerging biosensors for in vitro and in vivo DNA methylation assays in the past five years (2015-2020). Based on the signal types, the biosensors for in vitro DNA methylation assay are classified into five categories including fluorescent, electrochemical, colorimetric, surface enhanced Raman spectroscopy, mass spectrometry, and surface plasmon resonance biosensors, while the biosensors for in vivo DNA methylation assay mainly rely on fluorescent imaging. We review the strategies, features and applications of these biosensors, and provide a new insight into the challenges and future directions in this area.

Visual Detection of Fusion Genes by Ligation-Triggered Isothermal Exponential Amplification: A Point-of-Care Testing Method for Highly Specific and Sensitive Quantitation of Fusion Genes with a Smartphone

Fusion genes, playing a causal role in human tumorigenesis and developments, are deemed as gold standard molecular biomarkers in cancer diagnosis, therapy, and prognosis. A rapid, robust, and sensitive method of detection of fusion genes for point-of-care (POC) diagnosis is urgently needed. Here, taking the advantages of the superior specificity of the ligation reaction and the highly amplified efficiency of isothermal exponential amplification with a pH indicator, we developed a colorimetric method for visual detection of fusion genes with high sensitivity and specificity by the naked eye. More importantly, we first found that fusion genes can be accurately quantified in a wide dynamic range (2 zmol to 2 fmol) by an open-source app with a smartphone-assisted RGB (red, green, and blue value) reading mode. The proposed method for Visual detection of Fusion genes by Ligation-triggered Isothermal Exponential Amplification is termed Vis-Fusion LIEXA. We have demonstrated that the Vis-Fusion LIEXA is a practical and reliable method for accurate quantitative detection of the fusion gene in a complex biological sample at zmol level in 40 min only with a smartphone, thereby providing a user-friendly and point-of-care testing (POCT) tool for molecular diagnostics.