CHAPTER 12: Covalent and Non-covalent Conjugates of Oligonucleotides as Artificial Restriction DNA Cutters

Artificial enzymes for site-selective DNA scission are constructed from oligonucleotide conjugates and a Ce(IV)/EDTA complex which hydrolyses only single-stranded DNA. For site-selective scission of a single-stranded DNA substrate, a gap structure is formed at a target site with the use of two complementary oligonucleotide additives, which is selectively cut by Ce(IV)/EDTA. This site-selective scission is greatly promoted by attaching a multiphosphonate ligand (e.g. N,N,N′,N′-ethylenediaminetetrakis(methylenephosphonic acid)) to the oligonucleotide additives and recruiting Ce(IV)/EDTA to the scission site. The single-stranded overhang of human telomeres is also selectively hydrolysed by using a multiphosphonate–oligonucleotide conjugate which forms a G-quadruplex with the overhang. A similar strategy is applicable to site-selective scission of double-stranded DNA, in which single-stranded portions are formed at target sites in both strands by using peptide nucleic acid (PNA) and selectively hydrolysed by Ce(IV)/EDTA. The scission site of these artificial DNA cutters is determined by the Watson–Crick base-pairing rule, and thus both the sequence and the scission specificity can be freely tuned. The recombinant DNA, formed by connecting the scission fragments with appropriate DNA with the use of ligase, successfully expresses the corresponding protein. Recent attempts to prepare site-selective DNA cutters by oxidising a Ce(III) complex to the corresponding Ce(IV) complex are also described.