Synthesis of DNA-Binding Polyamides: Robust Solid-Phase Methods for Coupling Heterocyclic Aromatic Amino Acids

Small molecules that recognize double-stranded DNA have the capacity to modulate various cellular processes, including DNA replication and repair, gene expression, cell cycle regulation, and growth, and therefore may serve as treatments for cancers or various genetic diseases. Currently, most DNA-binding therapeutics target short sequences of DNA with rather low selectivity, causing deleterious effects in both diseased and healthy cells (1 ). Thus, the development of molecules that target longer, more cell-type-specific sequences of DNA is of great interest. In this chapter, a rapid solid-phase synthesis of hairpin polyamides, a promising class of minor groove binding agents developed by the Dervan group at Caltech, is described (2 ). The robust coupling methods of aromatic amino acids outlined facilitate the application of combinatorial methods to polyamides and their further development as pharmaceutical reagents.