Protein binding protection in combination with DNA masking for sensitive and reliable transcription factor detection

A CRISPR-Cas12a-based electrochemical biosensor for the detection of microphthalmia-associated transcription factor

A novel electrochemical biosensor that combines the CRISPR-Cas12a system with a gold electrode is reported for the rapid and sensitive detection of microphthalmia-associated transcription factor (MITF). The biosensor consists of a gold electrode modified with DNA1, which contains the target sequence of MITF and is labeled with ferrocene, an electroactive molecule. The biosensor also includes hairpin DNA, which has a binding site for MITF and can hybridize with helper DNA to form a double-stranded complex that activates CRISPR-Cas12a. When MITF is present, it binds to hairpin DNA and prevents its hybridization with helper DNA, thus inhibiting CRISPR-Cas12a activity and preserving the DPV signal of ferrocene. When MITF is absent, hairpin DNA hybridizes with helper DNA and activates CRISPR-Cas12a, which cleaves DNA1 and releases ferrocene, thus reducing the DPV signal. The biosensor can detect MITF with high sensitivity (with an LOD of 8.14 fM), specificity, and accuracy in various samples, such as cell nuclear extracts and human serum. The biosensor can also diagnose and monitor melanocyte-related diseases and melanin production. This work provides a simple, fast, sensitive, and cost-effective biosensor for MITF detection and a valuable tool for applications in genetic testing, disease diagnosis, and drug screening.

Recent progress on rapid diagnosis of COVID-19 by point-of-care testing platforms

The outbreak of COVID-19 has drawn great attention around the world. SARS-CoV-2 is a highly infectious virus with occult transmission by many mutations and a long incubation period. In particular, the emergence of asymptomatic infections has made the epidemic even more severe. Therefore, early diagnosis and timely management of suspected cases are essential measures to control the spread of the virus. Developing simple, portable, and accurate diagnostic techniques for SARS-CoV-2 is the key to epidemic prevention. The advantages of point-of-care testing technology make it play an increasingly important role in viral detection and screening. This review summarizes the point-of-care testing platforms developed by nucleic acid detection, immunological detection, and nanomaterial-based biosensors detection. Furthermore, this paper provides a prospect for designing future highly accurate, cheap, and convenient SARS-CoV-2 diagnostic technology.

Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets

Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

Combination of bidirectional strand displacement amplification with single-molecule detection for multiplexed DNA glycosylases assay

DNA glycosylases can initiate base excision repair pathway to repair endogenous DNA base damages for the maintenance of genome stability. Multiple DNA glycosylases exhibit abnormal in various diseases, and the simultaneous measurement of different DNA glycosylases is critical to clinical diagnosis and drug discovery. Herein, we take advantage of single-molecule detection and bidirectional strand displacement amplification (SDA) to simultaneously detect uracil DNA glycolase (UDG) and human alkyladenine DNA glycosylase (hAAG). We design a partial double-stranded DNA (dsDNA) substrate modified with specific recognition sites of UDG and hAAG. The dsDNA substrate is labeled with BHQ1 and BHQ2 at the 5'-ends and then hybridizes with the Cy3/Cy5-labeled reporter probes to obtain the BHQ1/Cy3 and BHQ2/Cy5 base pairs, resulting in the quenching of Cy3/Cy5 fluorescence by BHQ1/BHQ2 via fluorescence resonance energy transfer (FRET). When UDG and hAAG are present, they can induce the base excision repair reaction and subsequently initiate the bidirectional SDA amplification process, releasing the Cy5/Cy3-labeled reporter probes from the dsDNA substrate and consequently the recovery of Cy5 and Cy3 fluorescence, which can be measured by single-molecule detection, with Cy5 indicating UDG and Cy3 indicating hAAG. This method possesses high sensitivity and good selectivity with the capability of quantifying multiple DNA glycosylases at the single-cell level. Furthermore, it can be used to simultaneously screen DNA glycosylase inhibitors and determine enzyme kinetic parameters, with the potential of sensing various DNA/RNA enzymes by simple changing the recognition sites of DNA substrates.

A signal transduction approach for multiplexed detection of transcription factors by integrating DNA nanotechnology, multi-channeled isothermal amplification, and chromatography

The variation patterns of transcription factors (TFs) provide direct information for the states of cell populations, which is of significance for biomedical research and clinical diagnostics. Herein, we show that through multi-channeled isothermal amplification, it is feasible to connect DNA-based signal transduction with chromatography for multiplexed detection of TFs. The described system is referred to as "PAC" which includes three major steps: (i) Protection, which uses DNA-modified magnetic beads to capture TFs and converts the capturing event into triggering signal; (ii) Amplification, which receives the triggering signal and generate DNA reporters through multi-channeled extension and nicking of oligonucleotides; and (iii) Chromatography, which separates and detects the DNA reporters in liquid chromatography. The quantitative detection of five essential TFs includes p50, p53, AP-1, MITF, and c-Myc is realized in a multiplexed manner, with the lowest detection limit of 0.5 pM. PAC can also provide effective means to measure the above five TFs in real samples, including cultured cells, xenograft tumors, and blood-based liquid biopsy. This study not only established a solution for multiplexed measurement of TFs for molecular diagnostics, but also paved avenue for bridging the gap between DNA nanotechnology and chromatography.

Antibody free ELISA-like assay for the detection of transcription factors based on double-stranded DNA thermostability

Transcription factors (TFs) play critical roles in gene expression regulation and disease development. Herein we report a chemiluminescence assay for the detection of transcription factor based on double-stranded DNA thermostability.