Self assembly in biological systems is increasingly being recognised as an important phenomenon. We have examined two model systems: the cationic meso-substituted free base porphyrin derivative trans-bis-(4-N- methylpyridiniumyl)diphenyl porphyrin (t-H2P) and Hoechst 33258 (Hoechst) both of which were known to assemble on DNA. t-H2P self-assembles in solution under appropriate conditions, whereas Hoechst does not. By varying ionic strength and ligand:DNA mixing ratios, these features together with their different steric constraints have led to quite different DNA binding behaviour. Hoechst on poly[d(A-T)]2 stacks across the major groove, probably after filling its well established monomeric minor groove binding mode. By way of contrast the Hoechst/poly[d(G-C)]2 self-assembled aggregates involve partially intercalated molecules stacking in the major groove. The binding mode adopted by t-H2P with poly[d(A-T)] 2 and poly[d(G-C)]2 appears to be kinetically controlled and to be determined by the pre-existence of monomer binding and/or ligand stacks in solution. With poly[d(A-T)]2 the modes adopted both involve displacing the DNA bases to be more parallel than perpendicular to the helix axis. One is probably based on porphyrin intercalation and the other on minor groove binding. Resonance light scattering, linear dichroism, circular dichroism, normal absorption and fluorescence spectroscopies have been used to characterise the self-assembly in these systems.