Site-selective DNA hydrolysis by Ce(IV)-EDTA with the use of one oligonucleotide additive bearing two monophosphates.
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.
Chen
Wen
W
Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
Komiyama
Makoto
M
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
D002614:Chelating Agents; D009841:Oligonucleotides; D002563:Cerium; D004247:DNA; D004492:Edetic Acid