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

Abstract

An alternative photo-cross-linker having a D-threoninol skeleton instead of the 2′-deoxyribose backbone in 3-cyanovinylcarbazole (^CNVK) was investigated to improve the photoreactivity of photo-cross-linkers; the photo-cross-linking rate of 3-cyanovinylcarbazole with D-threoninol (^CNVD) was found to be greater than that of ^CNVK. Therefore, in this study, a novel photo-cross-linker having pyranocarbazole (^PCX) and D-threoninol instead of the 2′-deoxyribose backbone in ^PCX (^PCXD) was developed. The ^PCXD in double-stranded DNA photo-cross-linked to a pyrimidine base at the −1 position of a complementary strand similar to ^PCX. Furthermore, the photoreactivity of ^PCXD was significantly higher than that of ^PCX. The introduction of D-threoninol improved the reactivity of pyranocarbazole to cytosine, the use of ^PCXD 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.