Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex.
A new strategy for site-selective DNA hydrolysis, which takes advantage of the difference in reactivity between the phosphodiester linkages at the target site and the others, is presented. As the molecular scissors, homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (EDTA) complex is used without being bound to any sequence-recognizing moiety. When a gap structure is formed at the target site by using two short oligonucleotides and the composite is treated with the Ce(IV)/EDTA complex at pH 7.0 and 37 degrees C, the gap site in the substrate DNA is preferentially hydrolyzed over the double-stranded portion of the DNA. Site-selective DNA scission is also achieved by forming a bulge structure at the target site with the use of the appropriate oligonucleotide. These site-selective scissions are based on the following two factors: (i) the phosphodiester linkages in a single-stranded DNA are far more susceptible to the hydrolysis by the Ce(IV) complex than are the linkages in double-stranded DNA, and (ii) the phosphodiester linkages in the bulge sites are still more reactive than those in single-stranded DNA. In both cases, the addition of spermine significantly accelerates the scission.
D001483:Base Sequence; D001665:Binding Sites; D002563:Cerium / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004492:Edetic Acid / Q000737:chemistry*; D006868:Hydrolysis / Q000187:drug effects; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D013096:Spermine / Q000494:pharmacology
D013096:Spermine; D002563:Cerium; D004247:DNA; D004492:Edetic Acid