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

Abstract

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.

Keywords: C to U conversion; RNA editing; cyanovinylcarbazole; reversible photo-crosslinking.