DNA methylation plays an important role in development process which contributes to genome stability and also regulates gene expression and gene silencing. Detection of genome regions with altered 5-methylcytosine distribution at a genome-wide scale is very important for early detection of gene silencing related diseases. In the present study as a continuation of studies on DNA methylation, the interactions between graphene quantum dots (GQDs) and unmethylated and methylated deoxyribonucleic acid (DNA) fragment were investigated. Based on above interaction a novel GQDs-DNA nanoassembly was developed. Two types of DNA including unmethylated and methylated sequences were interacted with GQDs and contributed to the formation of unmethylated and methylated nanoassemlies. Analysis of the interaction indicated that the GQDs could bind to DNA fragments and led to different fluorescence pattern in two different mechanisms and could provide an efficient biosensing platform for label free and sensitive fluorescent assay of DNA. The excitation and emission wavelengths of experiment were 380 and 480 nm respectively. Fluorescence intensity of unmethylated DNA concentration were detectable from methylated DNA in linear range from 10.0-10M to 10.0-6M and the detection limit was estimated at 7.3 × 10-11 M. Above interaction was not observed in methylated DNA, indicated of distinguished interaction effect. Herein we further showed that GQDs could induce B-DNA to A-DNA form in methylated structure of DNA. The methylation sensitivity of the experiment was also testified by methylation sensitive restriction process. It was assumed that the involvement of methylation alteration in DNA structure could alter not only mechanism of DNA/GDQs interaction but also helical structure of DNA.