Study of porphyrin-modified liquid exfoliated graphene field-effect transistors for evaluating DNA methylation degree

The applications of graphene field-effect transistors (FETs) for monitoring DNA hybridization have been widely accepted; however, for evaluating DNA methylation degree, an emerging requirement of epigenetic research, no work has been found due to the difficulties in detecting 5-methylcytosine (5mC) sites along the genomic sequence as well as counting their amount (NmC). Herein, to achieve this, a strategy for exploiting a liquid exfoliated graphene (LEG)-based FET (LEG-FET) as a sensing platform was proposed. First, LEG-FETs were prepared and activated by tetra-4-aminophenyl-porphyrin (TAPP) for anchoring single-strand DNAs (ssDNAs). Second, the 5mC sites in ssDNA were recognized by the specifically absorbed 5mC antibody (5mCab) and transduced to the changed currents (ΔIDS) by LEG-FET according to the integration of the methylation-immuno sensing principle and FET's working mechanism. Briefly, more 5mCab molecules could be captured by more 5mC sites, resulting in larger ΔIDS. The TAPP effects on LEG-FET were analyzed by SEM, Raman, AFM, and XPS characterizations as well as electronic measurements. The validity of this LEG-FET sensing platform for evaluating DNA methylation degree was proven step by step; this included the examinations of the synthesized ssDNAs with the known NmC and real ssDNA samples, whose methylation degrees were pre-determined by the gold-standard method, which is based on tedious bisulphite sequence operations and expensive mass spectrometry technology. Moreover, theoretical explanations were also provided for the sensing mechanism in the proposed DNA methylation analytical components. In conclusion, the positive and linear relations of IDS changing ratio vs. NmC as well as the detection limit of one 5mC site indicate that TAPP-modified LEG-FET can provide an alternative analytical tool to realize fast and economical DNA methylation evaluation.