DNA photo-cross-linking using a pyranocarbazole-modified oligodeoxynucleotide with a d-threoninol linker

An alternative photo-cross-linker having a d-threoninol skeleton instead of the 2′-deoxyribose backbone in 3-cyanovinylcarbazole ((CNV)K) was investigated to improve the photoreactivity of photo-cross-linkers; the photo-cross-linking rate of 3-cyanovinylcarbazole with d-threoninol ((CNV)D) was found to be greater than that of (CNV)K. Therefore, in this study, a novel photo-cross-linker having pyranocarbazole ((PC)X) and d-threoninol instead of the 2′-deoxyribose backbone in (PC)X ((PCX)D) was developed. The (PCX)D in double-stranded DNA photo-cross-linked to a pyrimidine base at the −1 position of a complementary strand similar to (PC)X. Furthermore, the photoreactivity of (PCX)D was significantly higher than that of (PC)X. The introduction of d-threoninol improved the reactivity of pyranocarbazole to cytosine, the use of (PCX)D may extend the applicability of the photo-cross-linking reaction for DNA manipulation. In particular, this novel photo-cross-linker can contribute to the photochemical regulation of gene expression or biological events in a living cell.