Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy

Four genomic DNAs of differing GC content (Micrococcus luteus, 72% GC; Esch erichia coli, 50% GC; calf thymus, 42% GC; Clostridium perfringens, 27% ac) have been employed as targets of interaction by the cationic polyamines sp ermidine {[H3N(CH2)(3)NH2(CH2)(4)NH3](3+)) and spermine {[(CH2)(4)(NH2(CH2) (3)NH3)(2)](4+)). In solutions containing 60 mM DNA phosphate (similar to 2 0 mg DNA/ml) and either 1, 5 or 60 mM polyamine, only Raman bands associate d with the phosphates exhibit large spectral changes, demonstrating that B- DNA phosphates are the primary targets of interaction. Phosphate perturbati ons, which are independent of base composition, are consistent with a model of non-specific cation binding in which delocalized polyamines diffuse alo ng DNA while confined by the strong electrostatic potential gradient perpen dicular to the helix axis. This finding provides experimental support for m odels in which polyamine-induced DNA condensation is driven by non-specific electrostatic binding. The Raman spectra also demonstrate that major groov e sites (guanine N7 and thymine C5H(3)) are less affected than phosphates b y polyamine-DNA interactions. Modest dependence of polyamine binding on gen ome base composition suggests that sequence context plays only a secondary role in recognition. Importantly, the results demonstrate that polyamine bi nding has a negligible effect on the native B-form secondary structure, The capability of spermidine or spermine to bind and condense genomic B-DNA wi thout disrupting the native structure must be taken into account when consi dering DNA organization within bacterial nucleoids or cell nuclei.