Epigenetic Quantification of DNA 5-Hydroxymethylcytosine Using DNA Hybridization-Based Single-Molecule Immunofluorescent Imaging

Rapid and highly specific detection of site-specific 5-hydroxymethylcytosine based on peroxotungstate oxidation and mismatch ligation-based LAMP

We have developed a rapid and specific method for site-specific 5-hydroxymethylcytosine (5hmC) quantification at single-base resolution. This bisulfite-free method integrates the peroxotungstate oxidization with the mismatched probe-assisted ligation to guarantee the specificity. Moreover, the high-efficiency LAMP also makes the proposed method suitable for the detection of low-content samples.

A facile and highly specific mismatch ligation-based amplification platform for quantification of site-specific 5hmC at single base resolution in low-content samples.

Hydroxymethylation-Specific Ligation-Mediated Single Quantum Dot-Based Nanosensors for Sensitive Detection of 5-Hydroxymethylcytosine in Cancer Cells

5-Hydroxymethylcytosine (5hmC) modification is a key epigenetic regulator of cellular processes in mammalian cells, and its misregulation may lead to various diseases. Herein, we develop a hydroxymethylation-specific ligation-mediated single quantum dot (QD)-based fluorescence resonance energy transfer (FRET) nanosensor for sensitive quantification of 5hmC modification in cancer cells. We design a Cy5-modified signal probe and a biotinylated capture probe for the recognition of specific 5hmC-containing genes. 5hmC in target DNA can be selectively converted by T4 β-glucosyltransferase to produce a glycosyl-modified 5hmC, which cannot be cleaved by methylation-insensitive restriction enzyme MspI. The glycosylated 5hmC DNA may act as a template to ligate a signal probe and a capture probe, initiating hydroxymethylation-specific ligation to generate large amounts of biotin-/Cy5-modified single-stranded DNAs (ssDNAs). The assembly of biotin-/Cy5-modified ssDNAs onto a single QD through streptavidin-biotin interaction results in FRET and consequently the generation of a Cy5 signal. The nanosensor is very simple without the need for bisulfite treatment, radioactive reagents, and 5hmC-specific antibodies. Owing to excellent specificity and high amplification efficiency of hydroxymethylation-specific ligation and near-zero background of a single QD-based FRET, this nanosensor can quantify 5hmC DNA with a limit of detection of 33.61 aM and a wider linear range of 7 orders of magnitude, and it may discriminate the single-nucleotide difference among 5hmC, 5-methylcytosine, and unmodified cytosine. Moreover, this nanosensor can distinguish as low as a 0.001% 5hmC DNA in complex mixtures, and it can monitor the cellular 5hmC level and discriminate cancer cells from normal cells, holding great potential in biomedical research and clinical diagnostics.

A Fluorescent "Turn-On" Clutch Probe for Plasma Cell-Free DNA Identification from Lung Cancer Patients

Early diagnosis of cancer is of paramount significance for the therapeutic intervention of cancers. Although the detection of circulating cell-free DNA (cfDNA) has emerged as a promising, minimally invasive approach for early cancer diagnosis, there is an urgent need to develop a highly sensitive and rapid method to precisely identify plasma cfDNA from clinical samples. Herein, we report a robust fluorescent "turn-on" clutch probe based on non-emissive QDs-Ru complexes to rapidly recognize EGFR gene mutation in plasma cfDNA from lung cancer patients. In this system, the initially quenched emission of QDs is recovered while the red emission of Ru(II) complexes is switched on. This is because the Ru(II) complexes can specifically intercalate into the double-stranded DNA (dsDNA) to form Ru-dsDNA complexes and simultaneously liberate free QDs from the QDs-Ru complexes, which leads to the occurrence of an overlaid red fluorescence. In short, the fluorescent "turn-on" clutch probe offers a specific, rapid, and sensitive paradigm for the recognition of plasma cfDNA biomarkers from clinical samples, providing a convenient and low-cost approach for the early diagnosis of cancer and other gene-mutated diseases.

Epigenetic Quantification of 5-Hydroxymethylcytosine Signatures via Regulatable DNAzyme Motor Triggered by Strand Displacement Amplification

DNA methylation predominantly occurs within the CpG dinucleotide, which is the main epigenetic form of gene expression regulation in mammals. Genomic DNA with CpG sites has different sequence lengths and complex secondary structures, resulting in the complexity and diversity of the samples. Therefore, highly efficient quantification of DNA methylation in complex samples remains challenging. Herein, the regulatable DNAzyme motor triggered by strand displacement amplification (SDA) was designed to quantify 5-hydroxymethylcytosine (5hmC) signatures as a model. Briefly, the 5hmC sites as primary target were specifically labeled with DNA primers and converted into a large number of single-stranded DNA (secondary target) via the SDA reaction which could activate the DNAzyme motor. With the increase of secondary target, the DNAzyme motor gradually recovered its activity and could continuously cleave the track strands labeled quenching probes, causing electrochemiluminescence signal recovery and detection limit down to 0.49 fM for 5hmC. This strategy provides a new route to quantify natural base modifications in DNA and would hold promising potential for the early diagnosis of cancer and other diseases related to 5hmC.