Targeting of photooxidative damage on single-stranded DNA representing the bcr-abl chimeric gene using oligonucleotide-conjugates containing [Ru(phen)3]2+-like photosensitiser groups

Abstract

Photooxidative damage was induced predominantly at a single guanine base in a target DNA by irradiation (λ > 330 nm) in the presence of complementary oligodeoxynucleotide conjugates (ODN-5'-linker-[Ru(phen)₃]²⁺) (phen = 1,10-phenanthroline). The target DNA represents the b₂a₂ variant of the chimeric bcr-abl gene implicated in the pathogenesis of chronic myeloid leukaemia, and the sequence of the 17mer ODN component of the conjugate (³' G G T A G T T A T T C C T T C T T ⁵') was complementary to the junction region of the sense strand sequence of this oncogene. Two different conjugates were prepared, both of them by reaction of the appropriate succinimide ester with 5′-hexylamino-derivatised 17mer ODN. In Ru–ODN-1 (7) the linker was–(CH₂)₆-NHCO-bpyMe (-bpyMe = 4′-[4-methyl-2,2′-bipyridyl]), whereas in Ru–ODN-2 (13) it was –(CH₂)₆-NHCO–(CH₂)₃-CONH-phen. Photoexcitation of either of the conjugates when hybridised with the ³²P-5’-end-labelled target 34mer ⁵'T G A G²¹ C C C T T C A G C G G C C ³' (ODN binding site underlined) led to an alkali-labile site predominantly (> 90%) at the G²¹ base, which is at the junction of double-stranded and single-stranded regions of the hybrid. Greater yields were found with Ru–ODN-1 (7) than with Ru–ODN-2 (13). In contrast to this specific cleavage with Ru–ODN-1 (7) or Ru–ODN-2 (13), alkali-labile sites were generated at all guanines when the 34mer was photolysed in the presence of the free sensitiser [Ru(phen)₃]²⁺. Since [Ru(phen)₃]²⁺ was shown to react with 2′-deoxyguanosine to form the diastereomers of a spiroiminodihydantoin derivative (the product from ¹O₂ reaction), ¹O₂ might also be an oxidizing species in the case of Ru–ODN-1 (7) and Ru–ODN-2 (13). Therefore to determine the range of reaction, a series of ‘variant’ targets was prepared, in which G²¹ was replaced with a cytosine and a guanine substituted for a base further towards the 3′-end (e.g. Variant 3; ⁵′T G A C C A T C A A T A A G G A A G A A C C G²³ C T T C A G C G G³² C C ³′). While it was noted that efficient reaction took place at distances apparently remote from the photosensitiser (e.g. at G³², but not G²³ for Variant 3), this effect could be attributed to hairpinning of the single-stranded region of the target. These results are therefore consistent with the photooxidative damage being induced by a reaction close to the photosensitiser rather than by a diffusible species such as ¹O₂.