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

• Published in: Physical chemistry chemical physics : PCCP Vol. 11; no. 20; pp. 4025 - 4032
• Main Authors: Wei, Chunying, Jia, Guoqing, Zhou, Jun, Han, Gaoyi, Li, Can
• Format: Journal Article
• Language: English
• Published: Cambridge Royal Society of Chemistry 01.01.2009
• Subjects: Absorption; Buffers; Chemistry; Circular Dichroism; DNA - chemistry; Exact sciences and technology; G-Quadruplexes; General and physical chemistry; Humans; Melanins; Polyethylene Glycols - chemistry; Porphyrins - chemistry; Spectrometry, Fluorescence; Human; Binding; Nitrogen heterocycle; Stacking; Sandwich structure; Association constant; Fluorescence; Ethylene oxide polymer; Pyridinium compounds; Time resolved spectroscopy; Porphyrin; DNA; Binding mode; Porphyrin derivatives
• ISSN: 1463-9076; 1463-9084
• DOI: 10.1039/b901027k

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 AG(3)(T(2)AG(3))(3) G-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 AG(3)(T(2)AG(3))(3) G-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 AG(3)(T(2)AG(3))(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 AG(3)(T(2)AG(3))(3) G-quadruplex are non cooperative, the binding constants of two independent binding sites are 1.07 x 10(6) and 4.42 x 10(8) M(-1) for an antiparallel/parallel hybrid structure of AG(3)(T(2)AG(3))(3), 8.67 x 10(5) and 2.26 x 10(8) M(-1) for parallel-stranded AG(3)(T(2)AG(3))(3) G-quadruplex. Conversely, the two binding sites are cooperative for TPrPyP4, the apparent association constants are 5.58 x 10(6) and 1.24 x 10(7) M(-1) for parallel-stranded and antiparallel/parallel hybrid structures of AG(3)(T(2)AG(3))(3) G-quadruplex, respectively.