Sensitive lateral flow assay for bisulfite-free DNA methylation detection based on the restriction endonuclease GlaI and rolling circle amplification

New advances in signal amplification strategies for DNA methylation detection in vitro

5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.

Photoelectrochemical sensor based on AuNPs@WO3@TpPa-1-COF for quantification of DNA methylation levels

A "signal-off" photoelectrochemical (PEC) sensing platform has been designed for the ultrasensitive detection of DNA methylation levels and multiple methylated sites. The platform employs tungsten trioxide and TpPa-1-COF loaded by gold nanoparticle (AuNPs@WO3@TpPa-1-COF) composite material as the photoactive component and p-type reduced graphene (rGO) as an efficient quencher. The PEC signal of AuNPs@WO3@TpPa-1-COF composite is effectively quenched in the presence of p-type rGO, because p-type rGO can compete with AuNPs@WO3@TpPa-1-COF to deplete light energy and electron donors. In addition, a hybrid strand reaction (HCR) amplification strategy fixes more target DNA and then combines with rGO-modified anti-5-methylcytosine antibody to facilitate ultrasensitive DNA methylation detection. Under optimal conditions, DNA methylation can be measured within a linear concentration range of 10-14 to 10-8 M, with an exceptionally low detection limit of 0.19 fM (S/N = 3). At the same time, the platform can conduct quantitative determination of multi-site methylation, with the linear equation △I = 44.19LogA + 61.43, and the maximum number of methylation sites is 5. The sensor demonstrates high sensitivity, excellent selectivity, and satisfactory stability. Furthermore, the proposed signal-off PEC strategy was successfully employed to detect DNA methylation in spiked human serum samples, with recoveries ranging from 93.17 to 107.28% and relative standard deviation (RSD) ranging from 1.15 to 5.49%.

A review on recent advances in assays for DNMT1: a promising diagnostic biomarker for multiple human cancers

The abnormal expression of human DNA methyltransferases (DNMTs) is closely related with the occurrence and development of a wide range of human cancers. DNA (cytosine-5)-methyltransferase-1 (DNMT1) is the most abundant human DNA methyltransferase and is mainly responsible for genomic DNA methylation patterns. Abnormal expression of DNMT1 has been found in many kinds of tumors, and DNMT1 has become a valuable target for the diagnosis and drug therapy of diseases. Nowadays, DNMT1 has been found to be involved in multiple cancers such as pancreatic cancer, breast cancer, bladder cancer, lung cancer, gastric cancer and other cancers. In order to achieve early diagnosis and for scientific research, various analytical methods have been developed for qualitative or quantitative detection of low-abundance DNMT1 in biological samples and human tumor cells. Herein, we provide a brief explication of the research progress of DNMT1 involved in various cancer types. In addition, this review focuses on the types, principles, and applications of DNMT1 detection methods, and discusses the challenges and potential future directions of DNMT1 detection.

Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests

Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.

Self-accelerated DNA walker mediated electrochemical biosensor for rapid and ultrasensitive detection of microRNA

Herein, we developed a novel three-dimensional (3D) self-accelerated DNA walker (SADW) which progressively expedite walking rate by unlocking the more walking arm continuously in walker process to construct electrochemical biosensor for ultrasensitive detection of microRNA. Particularly, we skillfully introduced a target analogue sequence in the double-loop hairpin, which could be released in the walking process of SADW, then rapidly activating more silenced walking strands to achieve the continuous self-acceleration, resulting in the expedited reaction rate. Surprisingly, the average reaction rate of SADW was quite higher than that of traditional 3D self-circulating DNA walkers (DW) under pretty low target miRNA concentration, which is ascribed to the outstanding acceleration process of the SADW, readily conquering the major predicaments of DW in detecting target with traces concentration: slow reaction rate and low sensitivity. This way, the elaborated SADW is favorably applied in the ultrasensitive and rapid detection of miRNA-21 in tumor cancer cell lysates with a detection limit down to 5.81 aM which was far from lower than the detection limit of DW. This approach develops the novel generation of widespread strategy for the applications in clinic diagnose, biosensing assay, and DNA nanobiotechnology.

Ultrasensitive lateral flow biosensor based on PtAu@CNTs nanocomposite catalytic chromogenic signal amplification strategy for the detection of nucleic acid

A rapid and ultrasensitive lateral flow biosensor was developed, which based on gold and platinum nanoparticles-decorated carbon nanotubes (PtAu@CNTs) nanocomposite catalytic chromogenic signal amplification strategy for the detection of nucleic acid. Independent platinum and gold nanoparticles modified functional carbon nanotubes (PtAu@CNTs) were prepared by in-situ reduction. Sandwich-type hybridization reaction occurred between PtAu@CNTs-labeled DNA probe, target DNA and Biotin-modified DNA probes, which was captured on test zone of the strip. Accumulation of PtAu@CNTs nano-labels formed a characteristic colored band. After systematic optimization and catalytic chromogen, the naked eye detection limit of PtAu@CNTs-LFA was about 2 pM, and the theoretical detection limit of target DNA is calculated to be 0.43 pM according to the standard curve. The results indicates a rapid, sensitive and specific methods for DNA detection in biological samples, showing great promise for biomedical diagnosis in some malignant diseases in clinical application.

A novel one-pot fluorescence tagging and depyrimidination strategy for quantification of global DNA methylation

DNA methylation is intensively studied in medical science. Current HPLC methods for quantification of global DNA methylation involve digestion of a DNA sample and HPLC determination of both cytosine (C) and 5-methylcytosine (5mC) so that percentage of 5mC in total cytosine can be calculated as DNA methylation level. Herein we report a novel HPLC method based on a one-pot fluorescence tagging and depyrimidination reaction between DNA and chloroacetaldehyde (CAA) for highly sensitive quantification of global DNA methylation. In the one-pot reaction, C and 5mC residues in a DNA sequence react with CAA, forming fluorescent etheno-adducts that are then released from the sequence through depyrimidination. Interestingly, etheno-5mC (ε-5mC) is ∼20 times more fluorescent than ε-C and other ε-nucleobases resulting from the reaction, which greatly facilitates the quantification. Further, due to the tagging-induced increase in structural aromaticity, ε-nucleobases are far more separable by HPLC than intact nucleobases. The proposed HPLC method with fluorescence detection (HPLC-FD) is quick (i.e., < 1h per assay) and highly sensitive with a detection limit of 0.80 nM (or 250 fg on column) for 5mC. Using the method, DNA samples isolated from yeast, HCT-116 cells, and tissues were analyzed. Global DNA methylation was measured to be in the range from 0.35% to 2.23% in the samples analyzed. This sensitive method allowed accurate analyses of minute DNA samples (∼100 ng) isolated from milligrams of tissues.