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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 34, Number 7
BKCSDE 34(7)
July 20, 2013 

Sequence Dependent Binding Modes of the ΔΔ- and ΛΛ-binuclear Ru(II) Complexes to poly[d(G-C)2] and poly[d(A-T)2]
Nataraj Chitrapriya, Raeyeong Kim, Yoon Jung Jang, Dae Won Cho, Sung Wook Han, Seog K. Kim*
Bis Ru(II) complex, DNA, Sequence selectivity, Polarized spectroscopy, Binding geometry
The binding properties and sequence selectivities of ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ (bip = 4,4'-biphenylene (imidazo [4,4-f][1,10]phenanthroline) complexes with poly[d(A-T)2] and poly[d(G-C)2] were investigated using conventional spectroscopic methods. When bound to poly[d(A-T)2], a large positive circular dichroism (CD) spectrum was induced in absorption region of the bridging moiety for both the ΔΔ- and ΛΛ-[μ- Ru2(phen)4(bip)]4+ complexes, which suggested that the bridging moiety sits in the minor groove of the polynucleotide. As luminescence intensity increased, decay times became longer and complexes were wellprotected from the negatively charged iodide quencher compared to that in the absence of poly[d(A-T)2]. These luminescence measurements indicated that Ru(II) enantiomers were in a less polar environment compared to that in water and supported by minor groove binding. An angle of 45° between the molecular plane of the bridging moiety of the ΔΔ-[μ-Ru2(phen)4(bip)]4+ complex and the local DNA helix axis calculated from reduced linear dichroism (LDr) spectrum further supported the minor groove binding mode. In the case of ΛΛ- [μ-Ru2(phen)4(bip)]4+ complex, this angle was 55°, suggesting a tilt of DNA stem near the binding site and bridging moiety sit in the minor groove of the poly[d(A-T)2]. In contrast, neither ΔΔ- nor ΛΛ-[μ-Ru2(phen)4- (bip)]4+ complex produced significant CD or LDr signal in the absorption region of the bridging moiety. Luminescence measurements revealed that both the ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ complexes were partially accessible to the I− quencher. Furthermore, decay times became shorter when bis-Ru(II) complexes bound to poly[d(G-C)2]. These observations suggest that both the ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ complexes bind at the surface of poly[d(G-C)2], probably electrostatically to phosphate group. The results indicate that ΔΔ- and ΛΛ-[μ-Ru2(phen)4(bip)]4+ are able to discriminate between AT and GC base pairs.
2117 - 2124
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