A quantitative model of DNA fragments generated by ionizing radiation, and possible experimental applications

We derive an equation for observed frequencies of DNA fragments as a function of size. In this derivation, we consider an experimental system where fragments are generated by random, independent double-strand breaks on chromosomes (or other large DNA molecules) and then separated by size on agarose gels. When visualizing these fragments using Southern hybridization techniques (employing a site-specific probe), we predict an intensity distribution that has unusual properties. In particular, peaks in the fragment size distribution depend not only on standard breakage parameters, but also on the location of the hybridization site. Our model is consistent with experimental and theoretical results reported elsewhere, where measurements of peaks are used for the physical mapping of genes. Further, we propose that similar experiments might be suitable for precise measurements of the parameters of double-strand breakage (as an alternative to neutral filter elutions and neutral sucrose gradients) and for testing the assumption of random, independent breakage for different types of radiation.