Biogenic polyamines, putrescine, spermidine, and spermine, are ubiquitous cellular cations and exert multiple biological functions. Polyamine analogues mimic biogenic polyamines at macromolecular level but are unable to substitute for natural polyamines and maintain cell proliferation, indicating biomedical applications. The mechanistic differences in DNA binding mode between natural and synthetic polyamines have not been explored. The aim of this study was to examine the interaction of calf thymus DNA with three polyamine analogues, 1,11-diamino4,8-diazaundecane (333), 3,7,11,15-tetrazaheptadecane center dot 4HCl (BE-333), and 3,7,11,15,19-pentazahenicosane center dot 5HCl (BE-3333), using FTIR, UV-visible, and CD spectroscopy. Polyamine analogues bind with guanine and backbone PO2 group as major targets in DNA, whereas biogenic polyamines bind to major and minor grooves as well as to phosphate groups. Weaker interaction with DNA was observed for analogues with respect to biogenic polyamines, with K-333 = 1.90 (+/- 0.5) x 10(4) M-1, KBE-333 = 6.4 (+/- 1.7) x 10(4) M-1, KBE-3333 = 4.7 (+/- 1.4) x 10(4) M-1 compared to K-Spm = 2.3 (+/- 1.1) x 10(5) M-1, K-Spd = 1.4 (+/- 0.6) x 10(5) M-1, and K-Put = 1.02 (+/- 0.5) x 10(5) M-1. A partial B- to A-DNA transition was also provoked by analogues. These data suggest distinct differences in the binding of natural and synthetic polyamines with DNA.