DNA-organic hybrid molecular building blocks are generated by covalent conjugation of the carboxyl groups of protoporphyrin IX with the amine functional groups of modified DNA oligomers. The hybrids are used to engineer DNA nanocages by self-assembly of the complementary DNA-organic molecule conjugates. The nanocages were found to be lined up in head to tail fashion under the selective ionic strength of the solution. Computational approach revealed the area and volume acquired by each DNA-organic hybrid nanocages. © 2015 The Royal Society of Chemistry.