Analysis of Environment-Induced DNA Damage by Capillary Electrophoresis

Chemical pollutants, ionizing radiation, the products of aerobic metabolism and UV light are important metabolic and environmental factors contributing to DNA damage. Ionizing radiation, in particular, induces damage in the form of single-strand breaks, double-strand breaks, crosslinks, and associated conformational changes to the higher-order structure of DNA inside the cell. Several techniques, such as the single cell gel assay are used to analyze strand breakage in subpopulations of cells. Capillary electrophoresis (CE), by virtue of its high-separation efficiency, throughput, and automation has become recognized as a powerful tool to detect base, sequence, and structural changes in nanogram quantities of different DNA substrates. CE can also be combined with mass spectrometry (MS) to detect precursors to DNA strand breaks, i.e., DNA base modifications in human cancer cells (see refs. 1 and 2 ). In this chapter, we describe methods for the analysis of environment-induced structural changes in linear, plasmid, and genomic DNA. We describe the response of DNA to graded doses of laser or ionizing radiation as examples of how these methods can be used in a practical manner. Using CE to detect small radiation-induced fragments of DNA and conformational changes in large DNA fragments and plasmids provides a faster and more efficient alternative to other techniques such as standard and pulsed-field agarose gel electrophoresis.