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Issue 20, 2009
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Evidence for the binding mode of porphyrins to G-quadruplex DNA

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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.

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

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The article was received on 16 Jan 2009, accepted on 20 Feb 2009 and first published on 13 Mar 2009

Article type: Paper
DOI: 10.1039/B901027K
Citation: Phys. Chem. Chem. Phys., 2009,11, 4025-4032

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

    C. Wei, G. Jia, J. Zhou, G. Han and C. Li, Phys. Chem. Chem. Phys., 2009, 11, 4025
    DOI: 10.1039/B901027K

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