Investigating the intercalation efficacy of sinomenine with diverse DNA fragments to understand its regulatory role in DNA methylation levels.

DNA methylation is a crucial epigenetic modification associated with diseases. Current DNA methylation regulators like azacitidine often lack selectivity, causing side effects, necessitating the development of targeted agents. Our previous research showed sinomenine selectively regulates DNA methylation in the mPGES-1 promoter but not the COX-2 gene. This study reveals that sinomenine achieves selectivity through sequence-specific intercalation-a novel mechanism distinct from conventional DNMT inhibitors. Using ultrahigh-resolution fluorescence microscopy, we confirmed the distribution of sinomenine in THP-1 cell line. Spectroscopic assays demonstrated intercalation with DNA, where stronger interaction (higher Ksv values) enabled targeted methylation regulation. Molecular docking elucidated atomic-level binding details, and bioinformatic analysis supported pathway enrichment. In summary, our findings demonstrate that stronger DNA intercalation (higher Ksv values) enables target-specific methylation regulation, establishing sinomenine as a precise epigenetic modulator with fewer off-target effects compared with those of conventional DNMT inhibitors. The ability of sinomenine to selectively regulate DNA methylation through intercalation offers a novel strategy for targeting specific genes, potentially reducing side effects associated with current treatments. This study elucidates the mechanism underlying the regulation of selective DNA methylation by sinomenine as well as highlights its potential as a therapeutic agent for diseases associated with aberrant DNA methylation.