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

[Display omitted] •Studied the behavior of transforming of i-motif to hairpin DNA induced by anthracycline drugs using nanopore at the single-molecule level.•Captured the current signal of the intermediate state during the unfolding of i-motif into hairpin DNA, which is difficult to detect by conventional analytical methods.•Demonstrated the potential for developing sensors to specifically detect mitoxantrone among the three anthracycline drugs. 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.