Label free colorimetric and fluorimetric direct detection of methylated DNA based on silver nanoclusters for cancer early diagnosis

Epigenetic changes such as DNA methylation of CpG islands located in the promoter region of some tumor suppressor genes are very common in human diseases such as cancer. Detection of aberrant methylation pattern could serve as an excellent diagnostic approach. Recently, the direct detection of methylated DNA sequences without using chemical and enzymatic treatments or antibodies has received great deal of attentions. In this study, we report a colorimetric and fluorimetric technique for direct detection of DNA methylation. Here, the DNA is being used as an effective template for fluorescent silver nanoclusters formation without any chemical modification or DNA labeling. The sensitivity test showed that upon the addition of target methylated DNA, the fluorescence intensity is decreased in a linear range when the concentration of methylated DNA has increased from 2.0×10−9 to 6.3 ×10−7M with the detection limit of 9.4×10−10M. The optical and fluorescence spectral behaviors were highly reproducible and clearly discriminated between unmethylated, methylated and even partially methylated DNA in CpG rich sequences. The results were also reproducible when the human plasma was present in our assay system. •The colorimetric and fluorimetric method for DNA methylation detection was introduced.•Direct DNA methylation was performed without any chemical and enzymatic treatments.•DNA/Ag NCs were exploited as a new fluorescent probe for detection of methylated DNA.•This nanobiosensor had LOD of 9.4×10−10 M for determination of methylated DNA.•The proposed nanobiosensor showed significant reproducibility in human plasma sample.