Effects of synergistic/antagonistic interactions between spermidine (3+) and putrescine (2+) on gene expression through higher-order DNA structural modification

Polyamines are essential cationic biomolecules that interact with negatively charged biomolecules, such as DNA, RNA, and proteins, thereby modulating their structure and function. Although spermidine(3+) and spermine(4+) often act synergistically, studies have indicated that putrescine(2+) can act antagonistically toward spermidine and other polyamines. To elucidate the associated synergistic/competitive effects, we investigated how putrescine and spermidine, when present together, cause higher-order structural changes in DNA and gene expression. Cell-free luciferase assays revealed that putrescine and spermidine exerted either synergistic or antagonistic effects on gene expression depending on their concentration. Millimolar concentrations of putrescine increased gene expression when combined with spermidine, but higher concentrations (e.g., 10 mM) inhibited expression. Atomic force microscopy revealed that structural changes in DNA were linked to changes in gene expression activity. These characteristic effects on DNA conformation and gene expression caused by the coexistence of putrescine and spermidine are examined in terms of physicochemical correlations among charged species, including the higher-order structure of negatively charged DNA, polycationic polyamines, and small counterions. At relatively low concentrations of polyamines, the effective negative charge of DNA decreases because of the cooperative effect between putrescine and spermidine. In contrast, at higher concentrations, the antagonistic effect becomes apparent as competitive interaction arises through counterion translational entropy. Notably, such bimodal effects could constitute a relatively general mechanism in the solution environment of living matter.