Protoporphyrin IX (PPIX) selectively binds to the 3′-terminal G-quartets of G-quadruplex DNAs, forming stable 1:1 complexes. This study provides the first structural insights into the molecular recognition of G-quadruplex DNA by PPIX, highlighting its binding specificity and potential applications in nucleic acid-targeted therapies.

Protoporphyrin IX (PPIX), a naturally occurring porphyrin, exhibits selective molecular recognition of G-quadruplex (G4) DNA structures. Herein, the binding behavior toward all-parallel G4 DNAs is investigated using NMR spectroscopy. PPIX is found to selectively bind to the 3′-terminal G-quartets of tetrameric [d(TTAGGG)]₄ (6mer) and monomeric d(TAGGGTGGGTTGGGTGIG) (18mer(G17I)), forming stable 1:1 complexes with binding constants around 1 μM⁻¹. In contrast, only minimal spectral changes of PPIX are observed in the presence of [d(TTAGGGT)]₄ (6mer/T), suggesting that the 3′-terminal thymine impedes complex formation. These findings represent the first NMR-based structural characterization of PPIX–G4 DNA complexes and provide new insights into the molecular determinants of porphyrin selectivity for G-quadruplex targets, which may contribute to the development of porphyrin-based G-quadruplex targeting agents.