Artificial site-selective DNA cutters to manipulate single-stranded DNA

Abstract

Recent progress regarding the development of artificial site-selective DNA cutters by chemical approaches are reviewed herein, with a special focus on site-selective cutters for single-stranded DNA. We employ a Ce(IV)/EDTA complex to serve as the catalyst, because it efficiently and selectively cuts single-stranded DNA. Using two complementary oligonucleotide additives, a gap structure is formed at the target site in the single-stranded DNA substrate. Owing to the substrate specificity of Ce(IV)/EDTA, the gap site is preferentially hydrolyzed, resulting in a site-selective DNA scission. The scission site is easily determined using the Watson–Crick base-pairing rule; thus, both the sequence and scission specificity can be tuned according to demand. The site-selective scission is greatly promoted by attaching a multiphosphonate to the termini of the oligonucleotide additives and placing this ligand at the gap site. The scission fragments can be connected with foreign DNA using ligase, and the recombinant DNA expresses the corresponding protein in E. coli. No undesired side reactions (for example, depurination, deletion, insertion, oxidative damage of nucleobases and off-target scission) occur throughout the DNA treatment.