Ultra-acceleration of Photochemical Cytosine Deamination by Using a 5'-Phosphate-Substituted Oligodeoxyribonucleotide Probe Containing a 3-Cyanovinylcarbazole Nucleotide at Its 5'-End

Photochemical RNA Editing of C to U by Using Ultrafast Reversible RNA Photo-crosslinking in DNA/RNA Duplexes

RNA editing, which is used to edit nucleobases in RNA strands; is more feasible for use in medical applications than DNA editing. We previously reported the photochemical conversion of cytosine to uracil, which required photo-crosslinking, deamination, and photo-splitting. Here, we evaluated the influence of the bases surrounding the target cytosine on the conversion of cytosine to uracil in the RNA strand. The photo-crosslinker 3-carboxyvinylcarbazole(^OHV K), which is more hydrophilic than 3-cyanovinylcarbazole(^CNV K), 3-carboxyamidevinylcarbazole(^NH2V K), and 3-methoxy carbonylvinylcarbazole(^OMeV K), induced faster deamination of cytosine. Furthermore, inosine, which forms two hydrogen bonds with cytosine, was the most efficiently paired base for accelerating photochemical RNA editing. Upon evaluation of the conversion from cytosine to uracil in RNA, the use of oligodeoxynucleotides containing ^OHV K and inosine and the polarity of the bases surrounding the target cytosine were found to be crucial.

Effect of linker length on photo-cross-linking position mediated by click chemistry via [2 + 2] photocycloaddition†

Ultrafast reversible DNA/RNA photo-cross-linking is a powerful tool for regulating the target strand in living cells. In particular, 3-cyanovinylcarbazole (CNVK) and 3-cyanovinylcarbazole modified by D-threoninol (CNVD) can photo-cross-link to pyrimidine bases within a few seconds of photoirradiation. However, these photo-cross-linkers can only cross-link to the counter base if it is adjacent to the 5'-side (-1 position). In this study, we synthesized novel photo-cross-linkers with varying linker lengths capable of photo-cross-linking with pyrimidine bases at locations other than the -1 position via click chemistry. The photo-cross-linking site was dependent on linker length.