Polyamines are i-motif disruptors

Polyamines are vital polycations involved in diverse cellular processes and nucleic acid interactions. However, a precise molecular mechanism for their gene regulatory roles, particularly through specific DNA secondary structures, is unclear. We report that the biogenic polyamines spermine, spermidine, and putrescine selectively destabilize DNA i-motif structures. In silico docking predicted that polyamines exhibit a strong affinity for i-motifs over other DNA forms. Biophysical analyses, including circular dichroism, surface plasmon resonance, and thermal melting, confirmed polyamine-induced disruption of both telomeric (hTeloC) and promoter region i-motifs (e.g., HIF-1A, BCL2, VEGF-A), while leaving G4s and the corresponding duplex DNA largely unaffected. Crucially, immunofluorescence studies using an i-motif-recognizing antibody provided the first in cellulo evidence of reduced intranuclear i-motif formation following polyamine treatment. Transcriptomic profiling further demonstrated that putrescine treatment preferentially alters the expression of genes enriched with putative i-motif sequences in their promoter regions. Our findings establish a novel regulatory axis in which polyamines act as endogenous, structure-specific destabilizers of DNA i-motifs, directly affecting gene expression. This work provides a mechanistic insight into transcriptional control through DNA secondary structures and suggests new therapeutic strategies targeting polyamine-i-motif interactions.