Effect of nucleobase change on cytosine deamination through DNA photo-cross-linking reaction via 3-cyanovinylcarbazole nucleoside
Photo-chemical deamination of cytosine using 3-cyanovinylcarbazole nucleoside (CNVK) mediated photo-crosslinking is a technique for site-directed mutagenesis. Using the technique in vivo requires the elimination of high-temperature incubation step and rather the incubation should be carried out at physiological conditions. Thus, to improve the reactivity of CNVK mediated photo-cross-link induced deamination of cytosine at physiological conditions, the evaluation of base pairing in cytosine has been carried out with respect to its deamination. Guanine has been replaced with 4 different counter bases (inosine, 2-aminopurine, 5-nitroindole, and nebularine), showing distinct hydrogen bonding pattern with target cytosine, which were incorporated at -1 position with respect to CNVK in the CNVK-modified photo-responsive oligodeoxyribonucleotides to ascertain the role of hydrogen bonding in the deamination at physiological conditions. Among the counter bases, inosine has shown highest acceleration towards the photo-induced deamination reaction.