Distribution of strand breaks produced by Auger electrons in decay of I-125 in triplex DNA

In this study we investigate the possibility of using Auger electrons as a probing agent for the study of structures of nucleic acids. To this end, we present the distribution of breaks produced in strands of a DNA duplex and a tripler-forming oligonucleotide (TFO) carrying Auger emitting radionucli de I-125. The method of calculation includes use of a molecular model of pl asmid DNA duplex with bound TFO carrying a labelled I-125 at position C5 of a single deoxycytosine residue, a source of Auger spectra, Monte Carlo ele ctron track structure and the ensuing chemistry codes, to simulate the dist ribution of breaks produced in both strands of a plasmid DNA. Frequencies o f fragment length distributions were obtained for the TFO, the purine and t he pyrimidine strands. The frequency of breaks in the purine strand showed good correlation with the published experimental results, while that for th e pyrimidine strand is lower by a factor of 3. It is concluded that the tru e structure of tripler DNA map not be purely of B-form.