Electrical discrimination of lysine methylation states at the single-molecule level

Lysine methylation is an important epigenetic modification that regulates chromatin structure and gene expression. However, it is still difficult to distinguish its methylated states without labels at the single-molecule level. In this study, we investigate the discrimination of lysine methylation states using single-molecule tunneling measurements with gold nano-gap electrodes. The conductance decreases stepwise as the number of methyl groups increases, even though density functional theory (DFT) shows that all molecules have almost the same HOMO energy levels. This result suggests that conductance is not determined only by the electronic structure, but also by how the molecule is arranged between the electrodes. Statistical analysis of current signals shows that high-conductance events become less frequent after methylation, indicating fewer strongly coupled configurations. The relationship between current and molecular length also supports that transport depends on variations in molecular configurations. Machine learning analysis achieved an F-score of 0.76 for distinguishing methylated from unmethylated lysine. In contrast, distinguishing between mono-, di-, and trimethylated forms gave a lower F-score of 0.49, reflecting overlap in the signals. These results suggest that single-molecule tunneling currents are sensitive to stepwise lysine methylation states through differences in transient molecular configurations. This work demonstrates the potential of single-molecule tunneling measurements for label-free analysis of epigenetic modifications.