Multi-Sample Array Chip for DNA Modification Quantification
Introducing an advanced multi-sample array chip that enables precise quantification of epigenetic DNA modifications, including 5-hydroxymethylcytosine (5-hmC) and DNA damage. This technology bridges the gap between sensitivity and throughput, providing a robust platform for cancer diagnostics and personalized medicine.
Unmet Need
Current methods for analyzing DNA modifications suffer from limitations such as low sensitivity, high cost, and the requirement for large DNA samples. These challenges hinder their application in clinical diagnostics and the monitoring of conditions like cancer.
Our Solution
This cutting-edge technology employs a custom-designed multi-array slide chip with optically labeled DNA, enabling high-throughput and ultra-sensitive quantification of epigenetic markers. Using a combination of fluorescence-based detection and hydrophobic masking, the system provides accurate measurements from minimal DNA samples, even at concentrations as low as 0.004%.
Unique Advantages
• High Sensitivity: Detects DNA modifications at levels undetectable by traditional methods, including 5-hmC levels below 0.004%.
• Low Sample Requirement: Operates effectively with DNA quantities as small as 5–30 ng.
• Cost-Effective: Utilizes standard fluorescent slide readers found in most medical facilities.
• High Throughput: Simultaneously processes multiple samples with minimal operator expertise.
• Versatile Applications: Extends from clinical diagnostics to cancer treatment monitoring and epigenetic research.
Assay Workflow Overview:
Steps (A) DNA lesions from UV or oxidative damage are recognized by repair enzymes. (B) Enzymes excise the damaged site, leaving a DNA gap. (C) DNA polymerase fills the gap with fluorescent nucleotides (D) Labeled DNA is applied to a custom glass slide.(E) Slide is scanned. (F) Images are analyzed to measure DNA damage.
Imaging Results:
(A) Slide design: 90 wells hold 0.5–2 µL of DNA (20 ng). (B1, B2) UV-irradiated U2OS cells show increasing damage signals (green) and constant DNA levels (blue).
This fluorescence-based assay efficiently quantifies DNA damage and repair.
Potential Applications
• DNA Damage detection and accurate quantification: Toxicity studies, drug safety, environmental exposure. Enables tunable detection of specific DNA lesions: UV, oxidation, crosslinks, ssDNA breaks etc.
• Cancer Diagnostics: Early detection and staging of cancers, including colorectal, pancreatic, and blood cancers.
• Treatment Monitoring: Evaluate responses to therapies through dynamic changes in DNA modifications.
• Personalized Medicine: Tailored health monitoring using minimal and residual biopsy samples.
• Epigenetic Research: Explore correlations between DNA modifications and various diseases or conditions.
Status
• Precise detection of blood and colon cancers In vivo assessment of UV induced DNA damage and repair
• Quantifying DNA damage in human sperm
References:
1. International Journal of Cancer 146 (1), 115-122
2. Analytical Chemistry 2020 92 (14), 9887-9894
3. ChemBioChem 2023, 24, e202300400