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Chiral Selective Stacking of a Cationic Porphyrin along Z-Form Poly[d(A-T)2]
Yoon Mo Hwang1, Nayoung Kwon1, Seog K Kim1
1Department of Chemistry and ‡College of Basic Education, Yeungnam University , Dae-dong, Gyeongsan 38541, Gyeong-buk, Republic of Korea.
Abstract:
In this study, the binding mode of porphyrin-free single-stranded poly[d(AT)] and trans-BMPyP was observed in the Z-form trans-BMPyP-poly[d(A-T)2] complex induced by extensive stacking depending on the temperature and concentration through circular dichroism (CD). The Z-form trans-BMPyP-poly[d(A-T)2] complex (R = 0.30) retained the Z-form DNA structure at a low temperature (20 °C) by the trans-BMPyP molecules. When the temperature was increased to 60 °C, the DNA was almost unfolded as a single-stranded poly[d(AT)], but the extensive stacking binding mode of trans-BMPyP was maintained and the shape of the porphyrin Soret band was symmetrically changed in comparison with the shape of the Z-form DNA. However, when the temperature was raised to 80 °C, the extensive stacking binding mode of trans-BMPyP was also unfolded almost completely. The binding mode of the trans-BMPyP-single-stranded poly[d(AT)] complex was very similar to the already known binding mode of porphyrins and a double-stranded DNA. The binding mode was dependent on the concentration ratio ([porphyrin]/[DNA]): a monomeric binding mode at a concentration ratio of 0.04, a moderate groove binding mode at a concentration ratio between 0.08 and 0.16, and extensive stacking at a concentration ratio between 0.20 and 0.30. The same result was obtained when the temperature of the Z-form DNA (R = 0.30) was increased to 60 °C. However, those binding modes were not found in cis-BMPyP, which was because, in the extensive stacking of trans-BMPyP along the DNA skeleton, the distance between the two positive methylpyridine ions at the trans site and thymine, one of the DNA bases, is decreased, creating a much more hydrophobic environment. In addition, the poly AT sequences found from the CD spectra for the binding of trans-BMPyP-poly[d(A-T)2] and trans-BMPyP-poly[d(AT)] (R = 0.30) showed that both of them underwent effective extensive stacking and that the chirality of extensive stacking was dependent on the form of DNA.
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