Series of novel peptide-bridged phenanthridine-nucleobase conjugates were prepared by solid phase peptide synthesis, which allowed easy and fast tuning of structure properties. Compounds were fully characterized in aqueous medium, pointing out to intramolecularly stacked structures. The stacked phenanthridine-thymine-phenanthridine system revealed characteristic excimeric fluorescence band and very specific CD spectrum. Studied compounds interact with double stranded DNA by intercalation, whereby binding is to minor extent influenced by attached thymine and amino-acid sequence of the peptide backbone.