Unusual bending patterns of spermidine³⁺ bound to DNA double helix

Natural polyamines play a fundamental role in the cell cycle. Despite being recognized as the most abundant organic counterions of DNA in the cell nucleus, their interactions with DNA have not been fully characterized. In a recent work [S. Perepelytsya, T. Vasiliu, A. Laaksonen, L. Engelbrecht, G. Brancato, and F. Mocci, J. Molec. Liq. 389, 122828 (2023)], we have shown how the interactions between spermidine(3+) and the DNA double helix induce significant conformational variations in the polyamine molecule. Specifically, we found that DNA induces conformations that are not observed in solution. Following that study, we present here a detailed investigation of the most compact conformation of the polyamine, analyzing its connection to the interaction with the DNA duplex. The analysis reveals that anomalous bent conformations of the spermidine(3+) molecule result from the interaction of all three amino groups of the polyamine with the DNA phosphate groups on the minor groove side of the double helix. The changes in dihedral angles of the bent spermidine(3+) molecule can be explained in terms of conformational transformations of six- and seven-membered rings, analogous to cyclohexane and cycloheptane. The analysis of the position of spermidine(3+) molecule along the DNA surface reveals a sequence specificity of this binding mode with a marked preference for the narrow minor groove of A-tracts. The formation of the anomalous bent conformations of spermidine(3+) in the complex with the DNA double helix is expected to be of paramount importance in understanding the mechanisms underlying DNA's biological function.