[Complementary addressed modification of single-stranded DNA using a [Fe-EDTA] derivative of oligonucleotide]

A one-tube synthesis scheme for coupling EDTA residue to the 5'-terminus of unprotected oligonucleotides via propylenediamine linker is described. The EDTA derivative of oligonucleotide d(pTGACCCTCTTCCC)A forms a kinetically stable complex with Fe2+ ion. In the presence of ascorbic acid with O2 limiting, this complex modifies single-stranded DNA (a 302-mer) in a site-specific way near the target complementary nucleotide sequence. The DNA fragment can be then cleaved predominantly at modified pyrimidine nucleotides (hidden breaks) by hot piperidine treatment, whereas few direct breaks (i.e. without piperidine) occurs at this site. No autocleavage of the [Fe.EDTA]-oligonucleotide derivative is observed under the experiment's conditions.