Interactions of Hoechst 33258 (H33258) with two synthetic DNA polynucleotides, poly dA-poly dT and poly dG-poly dC, as well as natural calf thymus (ct) DNA were studied using surface-enhanced Raman spectroscopy (SERS). Given variety of stoichiometry dependent interactions, complexes were prepared in [H33258]/[DNA] molar ratios of 1/1, 1/5, and 1/10 in the silver colloidal suspension. Prior to analysis of binding modes with DNA polynucleotides, aggregation tendency of the dye in the silver colloid was studied in the concentration range 1 Â 10 À6 -1 Â 10 À4 mol/L. The SERS spectra distinctive of aggregated and monomeric H33258 species were obtained, additionally indicating the form of the molecules bound to DNA. The obtained SERS spectra of H33258 with homo-polymeric polynucleotides implied a deep insertion of the molecules into the AT minor groove, and a partial intercalation between the GC base pairs achieved by the access through the GC major groove. Spectral characteristics of the dye dominated in the spectra of the complexes with ct-DNA, most likely due to random AT and GC sequences of the long natural nucleic acid, affecting uniform binding of the dye and consequently the adsorption of the H33258/DNA complex onto the enhancing metallic surface.