RADIOPROBING OF DNA - DISTRIBUTION OF DNA BREAKS PRODUCED BY DECAY OFI-125 INCORPORATED INTO A TRIPLEX-FORMING OLIGONUCLEOTIDE CORRELATES WITH GEOMETRY OF THE TRIPLEX

The distribution of breaks produced in both strands of a DNA duplex by the decay of I-125 carried by a tripler-forming DNA oligonucleotide w as studied at single nucleotide resolution. The I-125 atom was located in the C5 position of a single cytosine residue of an oligonucleotide designed to form a triple helix with the target sequence duplex, The majority of the breaks (90%) are located within 10 bp around the decay site, The addition of the free radical scavenger DMSO produces an ins ignificant effect on the yield and distribution of the breaks. These r esults suggest that the majority of these breaks are produced by the d irect action of radiation and are not mediated by diffusible free radi cals, The frequency of breaks in the purine strand was two times highe r that in the pyrimidine strand, This asymmetry in the yield of breaks correlates with the geometry of this type of tripler; the C5 of the c ytosine in the third strand is closer to the sugar-phosphate backbone of the purine strand, Moreover, study of molecular models shows that t he yield of breaks at individual bases correlates with distance from t he I-125 decay site. We suggest the possible use of I-125 decay as a p robe for the structure of nucleic acids and nucleoprotein complexes.