Greening the Solid-Phase Peptide Synthesis of the First Bicyclic Analogue of the Arc Repressor and Its Binding to DNA

Biological macromolecules such as proteins often interact with double-stranded DNA through the formation of hydrogen bonds in grooves, thereby modulating the accessibility of transcription factors to specific DNA sequences. Since the primary sequence of the arc repressor responsible for DNA binding and the associated 3D conformational requirements are well characterized, we have designed and synthesized a bicyclic analogue by ultrasound-assisted solid-phase peptide synthesis using a green approach. This new molecular entity was characterized by circular dichroism to verify the β-turn conformation and by a series of NMR experiments to elucidate its 3D structure. Its interaction with DNA oligomers containing the TAGA box was evaluated by using a battery of DNA displacement assays. Fluorescence quenching experiments revealed the close proximity between tryptophan residues and DNA bases, supporting the peptide–DNA interaction. Overall, the data demonstrate that this bicyclic β-sheet arc mimetic engages DNA with sequence selectivity, and to our knowledge, this represents the first report of such a design exhibiting topological preference for DNA grooves.