EFFECT OF RADIONUCLIDE LINKER STRUCTURE ON DNA CLEAVAGE BY I-125 LABELED OLIGONUCLEOTIDES

We studied the yield and distribution of DNA strand breaks produced by decay of I-125 introduced into triplex-forming and duplex-forming oli godeoxyribonucleotide (ODNs) through linkers of various lengths. ODNs were prepared with I-125 attached at the 5'-end with a long linker or to an internal nucleotide position with a short linker, The I-125-ODNs were hybridized to either a single-stranded target to form duplexes o r to a double-stranded target to form triplexes, After decay accumulat ion, the duplex and tripler samples were assayed for strand breaks in a sequencing gel, The yield of strand breaks per decay was 0.34 for du plex with the 5'-modified ODN and 0.66 for duplex with internally modi fied ODN, The tripler samples with internal I-125 have different yield s of DNA breaks in the pyrimidine and purine strands, 0.16 and 0.37, r espectively, The yield of DNA breaks in the pyrimidine strand of the t ripler with the 5'-modified ODN is 0.46, The majority of breaks are lo cated within 5 nucleotides from the decay site, The yield of strand cl eavage per decay of I-125 was nearly two-fold lower with the described linkers in comparison with the results obtained when I-125 is directl y attached to the C-5 position of cytosine, Nevertheless, the rapid io dination procedure reported here combined with the possibility of mult iple incorporations of I-125 On the linkers makes such I-125-ODNs prom ising agents for sequence-specific cleavage of DNA.