A robust procedure for removing background damage in assays of radiation-induced DNA fragment distributions

Radiat Res. 2006 Dec;166(6):908-16. doi: 10.1667/RR0663.1.


The non-random distribution of DNA breakage in PFGE (pulsed-field gel electrophoresis) experiments poses a problem of proper subtraction of the background DNA damage to obtain a fragment-size distribution due to radiation only. A naive bin-to-bin subtraction of the background signal will not result in the right DNA mass distribution histogram. This problem could become more pronounced for high-LET (linear energy transfer) radiation, because the fragment-size distribution manifests a higher frequency of smaller fragments. Previous systematic subtraction methods have been based on random breakage, appropriate for low-LET radiation. Moreover, an investigation is needed to determine whether the background breakage is itself random or non-random. We consider two limiting cases: (1) the background damage is present in all cells, and (2) it is present in only a small subset of cells, while other cells are not contributing to the background DNA fragmentation. We give a generalized formalism based on stochastic processes for the subtraction of the background damage in PFGE experiments for any LET and apply it to two sets of PFGE data for iron ions.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Artifacts*
  • Background Radiation*
  • Biological Assay / methods*
  • Computer Simulation
  • DNA / radiation effects*
  • DNA Fragmentation / radiation effects*
  • Dose-Response Relationship, Radiation
  • Models, Genetic*
  • Models, Statistical
  • Radiation Dosage
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Statistical Distributions


  • DNA