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Nucleic Acids Research, 2000, Vol. 28, No. 17 3379-3385
© 2000 Oxford University Press

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

Hong Deng, Victor A. Bloomfield, James M. Benevides1 and George J. Thomas Jr1,*

Department of Biochemistry, University of Minnesota, St Paul, MN 55108, USA and 1Division of Cell Biology and Biophysics, School of Biological Sciences, BSB 403, University of Missouri-Kansas City, 5100 Rockhill Road, Kansas City, MO 64110, USA

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. Modest dependence of polyamine binding on genome base composition suggests that sequence context plays only a secondary role in recognition. Importantly, the results demonstrate that polyamine binding has a negligible effect on the native B-form secondary structure. The capability of spermidine or spermine to bind and condense genomic B-DNA without disrupting the native structure must be taken into account when considering DNA organization within bacterial nucleoids or cell nuclei.

* To whom correspondence should be addressed. Tel: +1 816 235 5247; Fax: +1 816 235 1503; Email: thomasgj@umkc.edu


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