title: Site-selective DNA hydrolysis by Ce(IV)-EDTA with the use of one oligonucleotide additive bearing two monophosphates.
abstract: Two deoxyuridine derivatives each bearing a monophosphate group at the 5-position with a C3 linker, were incorporated into an oligonucleotide. By using this modified oligonucleotide, a bulge was formed at a predetermined position in a DNA substrate, and two monophosphate groups were placed at both junctions of the bulge. Upon treatment of the mixture with Ce(IV)-EDTA at pH 7.0, the phosphodiester linkages at the bulge site were selectively and efficiently hydrolyzed. The monophosphate groups introduced into the bulge site greatly accelerated site-selective DNA scission. Compared with the previously reported two-additive system, which combines two oligonucleotide additives each with a monophosphate at their termini, the present one-additive system is simpler and more convenient. Furthermore, site-selective DNA hydrolysis by using this one-additive system is successful even at high reaction temperatures (e.g., 55 degrees C). This reflects the thermodynamic stability of the duplexes formed between the substrate and the additive DNA.
authors.affiliation: Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
authors.forename: Wen
authors.initials: W
authors.lastname: Chen
authors.forename: Makoto
authors.initials: M
authors.lastname: Komiyama
mesh_terms: D001483:Base Sequence; D002563:Cerium / Q000737:chemistry*; D002614:Chelating Agents / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004492:Edetic Acid / Q000737:chemistry*; D024202:Electrophoretic Mobility Shift Assay; D006868:Hydrolysis; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000737:chemistry*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D002614:Chelating Agents; D009841:Oligonucleotides; D002563:Cerium; D004247:DNA; D004492:Edetic Acid