The surface-enhanced Raman scattering (SERS) spectra of aclacinomycin, saintopin, and their complexes with DNA recorded at the very low (ca. 10(-7) M) concentration allowed us to obtain, by the analysis of deuteration and pH effects, a vibrational assignment of the SERS active modes for both chromophores. We interpret the SERS spectra of aclacinomycin/DNA complex as indicating that the chromophore is stabilized inside double-stranded helix by the hydrogen bond between OH group of the chelate-like system of aclacinomycin (Figure 1) and functional group (probably, free C=O group of thymine) of DNA. The structural model of the complex is proposed and found to be consistent with NMR studies published before. This model is discussed in terms of data for daunomycin and adriamycin complexes with DNA fragments already obtained from X-ray measurements. In contrast to aclacinomycin, the binding mode of partial intercalation has been found to be preferential for saintopin chromophore. The free carbonyl group and a part of the chelate system (Figure 1) are both buried in the interior of DNA. However, the periphery hydroxyl group is shown to be still accessible to the silver surface upon the chromophore intercalation. No evidence for redistribution of intramolecular hydrogen bonds of the chromophore, or formation of new hydrogen bonds between saintopin and functional groups of DNA has been found. Differences between aclacinomycin and saintopin DNA intercalation modes revealed by the SERS spectroscopic data are considered in connection with their biological effects, especially within a process in which recognition of DNA by enzymes such as DNA topoisomerases I and II occurs.