Saporins are enzymes belonging to the PNAG class (polynucleotide: adenosine glycosidase), plant enzymes commonly known as ribosome-inactivating proteins (RIP), as a result of their property of irreversibly damaging eukaryotic ribosomes. Direct imaging with tapping-mode atomic force microscopy (AFM) has been used to study pGEM-4Z plasmid DNA binding to the saporin-SO6 (isoform from Saponaria officinalis seeds). Saporin wrapped the plasmidic DNA, and distribution of the enzyme molecules along the DNA chain was markedly variable; plasmid digested with saporin-SO6 appeared fragmented or topologically modified. The supercoiled DNA strands were cleaved, giving rise to a linearized form and to relaxed forms. Electrophoretic analysis of the effect of standard preparations of saporin-SO6 on pGEM-4S confirmed the presence of DNA strand-cleaving activity.