Four genomic DNAs of differing GC content (Micrococcus luteus, 72% GC;Escherichia coli, 50% GC; calf thymus, 42% GC; Clostridium perfringens, 27% GC) have been employed as targets of interaction by the cationic polyamines spermidine {[H3N(CH2)3NH2(CH2)4NH3]3+} and spermine {[(CH2)4(NH2(CH2)3NH3)2]4+}.
In solutions containing 60 mM DNA phosphate (~20 mg DNA/ml) and either 1, 5 or 60 mM polyamine, only Raman bands associated with the phosphates exhibit large spectral changes, demonstrating that B-DNA phosphates are the primary targets of interaction.
Phosphate perturbations, which are independent of base composition, are consistent with a model of non-specific cation binding in which delocalized polyamines diffuse along DNA while confined by the strong electrostatic potential gradient perpendicular to the helix axis
This finding provides experimental support for models in which polyamine-induced DNA condensation is driven by non-specific electrostatic binding.
The Raman spectra also demonstrate that major groove sites (guanine N7 and thymine C5H3) are less affected than phosphates by polyamine–DNA interactions.