Photosensitized Generation of Singlet Oxygen (1O2) from Pyropheophorbide a Specifically Bound to All Parallel-Stranded G-Quadruplex DNAs.

Pyropheophorbide a (Pyro-a), a chlorophyll metabolite, is a potential photosensitizer for photodynamic therapy (PDT), but little is known about its interaction with the target molecules for PDT, e.g., nucleic acids. Elucidation of the interaction between photosensitizers and nucleic acids will help us understand the initial process of PDT at the molecular level and hence to develop photosensitizing agents. We found that pyro-a forms a 1:1 complex with an all parallel-stranded G-quadruplex DNA and that pyro-a in the complex exhibits a quantum yield for singlet oxygen generation, with excitation at 664 nm, higher by a factor of ∼10 than that of pyro-a in an aqueous solution. These findings provided novel insights into molecular design of pyro-a-based photosensitizers to enhance their PDT efficacy.

Structural and functional characterization of complexes between heme and dimeric parallel G-quadruplex DNAs.

Heme has been receiving considerable interest as a prosthetic group of ribozymes and deoxyribozymes, because heme-bound nucleic acids exhibit peroxidase-like catalytic activities (Travascio, P., Li, Y., and Sen, D. (1998) Chem. Biol, 5, 505-517). The interaction of heme with dimeric G-quadruplexes formed from d(TAGGGTTAGGGT) and d(TAGGGTTAGGGA) has been characterized to gain a deeper understanding of the molecular recognition of G-quadruplex DNAs by heme. We found that heme binds selectively to the 3'-terminal G-quartet of a dimeric parallel G-quadruplex of d(TAGGGTTAGGGT), whereas binding of heme to a dimeric antiparallel G-quadruplex of d(TAGGGTTAGGGA) does not occur, suggesting that an orderly arrangement of the constituent guanine deoxyribose rings, with respect to the G-quartet plane, is crucial for the binding of heme to the DNA. The preferential binding of heme to the 3'-terminal G-quartet of parallel G-quadruplex DNAs allowed a systematic modification of the heme environment in the complex through the DNA sequence. The activity of the complexes was found to increase with increasing number of adenine bases adjacent to the heme in the complexes, possibly due to improvement of the accessibility of aromatic substrate, i.e., 10-acetyl-3,7-dihydroxyphenoxazine, to the heme, and an increase in the frequency of appearance of a specific orientation of the adenine bases, with respect to the heme, optimized for its activity as an acid-base catalyst to enhance the peroxidase activity of the complex.

Stepwise binding of a cationic phthalocyanine derivative to an all parallel-stranded tetrameric G-quadruplex DNA.

Interaction between an Ga(III) phthalocyanine (Pc) derivative bearing eight N-methylpyridinium groups at peripheral ß-positions (2,3,6,7,10,11,14,15-octakis-[N-methyl-(4-methylpyridinium-3-yloxy)phthalocyaninato] chloro gallium(III) iodide (GaPc)) and an all parallel-stranded tetrameric G-quadruplex formed from a heptanucleotide d(TTAGGGT) ([d(TTAGGGT)]4) has been investigated to elucidate the molecular recognition of G-quadruplex DNA by the Pc derivative, which provides a useful insight as to the design of G-quadruplex ligands suitable for various in vitro and in vivo applications. We found that GaPc binds to the A3G4 and G6T7 steps of [d(TTAGGGT)]4, with binding constants of (21 ± 2) × 106 and (0.09 ± 0.06) × 106 M-1, respectively, to form a 2:1 complex. Obviously, upon the binding of GaPc to each of the sites, the π-π stacking and electrostatic interactions of the Pc moiety and positively-charged side chains of GaPc with a G-quartet and the negatively-charged phosphate groups in nearby phosphodiester bonds of the DNA, respectively, are major driving forces for the complexation. Considering the similarity in the local structural environment between the A3G4 and G6T7 steps of [d(TTAGGGT)]4, the remarkably large difference in the GaPc-binding affinity between them is most likely accounted for by the effect of the polarity of the GaPc-binding site on the intermolecular electrostatic interaction. This finding provides valuable insights as to the design of Pc derivatives as G-quadruplex ligands.