Chemical RNA Editing for Genetic Restoration: The Relationship between the Structure and Deamination Efficiency of Carboxyvinyldeoxyuridine Oligodeoxynucleotides

Oligodeoxynucleotides containing 5-carboxyvinyl-2'-deoxyuridine ((CV) U-containing ODNs) for successful site-specific transition of cytosine to uridine by photo-cross-linking have three parts: the complementary sequence, hairpin loop and the 5'-terminal photoresponsive nucleobase (CV) U. Photo-cross-linking with (CV) U-containing ODNs was performed using UV (366 nm) irradiation, followed by heat treatment for deamination. The cross-linked nucleotide was cleaved by photosplitting (UV, 312 nm). The products were analyzed using restriction fragment length polymorphism and fluorescence measurements. In previous studies, we have successfully performed site-directed photochemical base substitution toward a synthetic single-stranded 100-mer ODN target (ss100-nt) and in vitro-synthesized full-length blue fluorescent protein mRNA as targets. Although the efficiency of C-to-U site-specific transition strongly depends on the sequence and structure of (CV) U-containing ODNs, the relationship between (CV) U-containing ODNs and the deamination efficiency of targeted editing remains unclear. Therefore, in this study, we attempted to identify the optimal sequence and primary structure of (CV) U-containing ODNs for site-directed specific transition. To evaluate the structure-deamination efficiency relationship, a series of eight (CV) U-containing ODNs were designed and studied. We showed that the optimal deamination efficiency was achieved with ODNs having a complementary sequence length slightly more than 14 nt and a hairpin length of 9 nt.