Nanopore-based single-molecule investigation of the effects of anthracycline anticancer drugs on i-motif

Intercalated binding of anthracycline anticancer drugs to DNA is associated with anticancer mechanisms. The i-motif, a cytosine-rich DNA secondary structure found in the promoter region of oncogenes, is a primary target for anticancer drugs action. Therefore, it is significant to study the interaction between anthracycline drugs and i-motif for cancer therapy using simple, rapid and low-cost analytical methods. Here, we utilized α-HL protein nanopore, which offers high sensitivity and high signal-to-noise ratio to investigate the conformational transition of human telomere i-motif induced by various anthracycline drugs at the single-molecule level. Our results revealed for the first time that anthracyclines drugs could induced the unfolding of i-motif into hairpin DNA. Additionally, our experiment captured the current signal of the intermediate state during the unfolding of i-motif into hairpin DNA, a signal difficult to obtain by conventional analytical tools such as circular dichroism (CD) and UV–visible spectroscopy (UV–vis). This research provides a novel tool for investigating the interaction between small molecule and DNA and lays the foundation for future screening of drugs acting on i-motif targets, as well as analyzing their therapeutic mechanism.