Peptide nucleic acids (PNAs) amphiphiles have been reported to assemble into different nanostructures; however, there is immense untapped potential to control their supramolecular assemblies by altering their lipid chain. Here, we functionalized di-guanine PNA with various hydrophobic appendages, namely dodecyl, p-dodecylbenzoyl and pentadecyl phenol groups, to investigate the effect of aromatic linkers, long alkyl and alkoxyl substituents on hierarchical self-assembly of di-guanine PNA. Systematic electron microscopy and atomic force microscopy studies revealed that while all three derivatives of di-guanine-PNA formed nanospheres, only nanospheres of dodecylamide and pentadecyl phenol derivatives matured into nanorods, these later formed higher order fractal assemblies. Furthermore, we observed that inclusion of a positively charged lysine at the C-terminus prevented fractal assembly, possibly due to electrostatic repulsion between the head groups. Thus, the findings of the present work might guide rational design of PNA amphiphiles to obtain specific self-assembled morphology.[a] Dr.