Evidence for the binding mode of porphyrins to G-quadruplex DNA

Abstract

Interactions of porphyrin derivatives 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin (TMPyP4) and 5,10,15,20-tetrakis(N-propylpyridinium-4-yl)-21H,23H-porphyrin (TPrPyP4) with human telomeric AG₃(T₂AG₃)₃G-quadruplex DNAs in 150 mM K⁺-containing buffer in the presence or absence of 40% molecular crowding agent poly(ethylene glycol) (PEG 200) were studied by absorption titration fitting and time-resolved fluorescence spectroscopy. The results show that two TMPyP4 (or TPrPyP4) molecules bind to antiparallel/parallel hybrid structure of AG₃(T₂AG₃)₃G-quadruplex by end-stacking and outside groove binding modes in the absence of PEG. Interestingly, in the presence of PEG one porphyrin molecule is stacked between two parallel AG₃(T₂AG₃)₃ G- quadruplexes to form a sandwich structure, another porphyrin molecule is bound to the groove of the G-quadruplex. The interactions of TMPyP4 with different structures of AG₃(T₂AG₃)₃G-quadruplex are non cooperative, the binding constants of two independent binding sites are 1.07 × 10⁶ and 4.42 × 10⁸ M⁻¹ for an antiparallel/parallel hybrid structure of AG₃(T₂AG₃)₃, 8.67 × 10⁵ and 2.26 × 10⁸ M⁻¹ for parallel-stranded AG₃(T₂AG₃)₃G-quadruplex. Conversely, the two binding sites are cooperative for TPrPyP4, the apparent association constants are 5.58 × 10⁶ and 1.24 × 10⁷ M⁻¹ for parallel-stranded and antiparallel/parallel hybrid structures of AG₃(T₂AG₃)₃G-quadruplex, respectively.