Described are the syntheses of 15 macrocyclic peptides designed to trap Holliday junctions (HJs) in bacteria during site-specific and homologous recombination. This leads to inhibiting bacterial growth. These second generation macrocycles were based on the C-2 symmetrical HJ. They were synthesized using a strategy that permits elucidation of the amino acid role in binding HJs. The syntheses of these macrocycles are an important step in the development of a new class of antibiotics.