Fluorescence enhancement of silver nanocluster at intrastrand of a 12C-loop in presence of methylated region of sept 9 promoter

Highlights: • Detection of methylated DNA by fluorescence turn on is developed. • Target sequence is from Sept9 promoter region. • Detection limit of methylated strand was 7.6 × 10^-8 M. • Silver ions affect the structure of methylated and non-methylated DNA. • Trun on in NC fluorescence is depended on methylated DNA sequence. - Abstract: Determining methylation state of a particular DNA sequence is an essential task in many epigenetic investigations. Here a facile method based on silver nanocluster (AgNCs) fluorescence enhancement is presented. Target sequences were selected from Sept9 promoter region that its hypermethylation is demonstrated as a reliable biomarker of colorectal cancer. Probe DNA was complementary to a 25 nucleotide of the target region and possessed twelve additional cytosines in the middle to grant the formation of AgNCs. After probe strands were hybridized with methylated and non-methylated targets separately, AgNCs were synthesized, and their fluorescence intensities were recorded. Fluorescence intensity enhanced when the target strands were methylated and quenched when they were non-methylated. The Linear range of fluorescence enhancement was from 1.0 × 10^-7 M to 5.0 × 10^-7 M with the detection limit of 7.6 × 10^-8 M. Sensor specificity was checked with non-complementary strands with the maximum similarity of 40%. Further experiments explored various characteristics of methylated and non-methylated DNAs carrying AgNC and indicated that structure of methylated and non-methylated DNAs was affected differently by silver ions that could then influence AgNC fluorescence. This effect was strongly sequence-dependent, and either fluorescence enhancement or quenching was observed with two different sequences.