After lysis of cells in the gel, incubate with a repair enzyme that will convert particular base lesions to DNA breaks. Compare the breaks seen with the enzyme with the breaks seen on incubation for the same time with buffer but no enzyme. Enzymes: Endonuclease III converts oxidised pyrimidines to breaks; formamidopyrimidine DNA glycosylase (FPG) converts 8-oxoguanine and some other oxidised purines to breaks; AlkA converts alkylated bases to AP (apurinic/apyrimidinic) sites; T4 endonuclease V converts cyclobutane pyrimidine dimers to breaks. Some of these enzymes have an associated AP lyase or endonuclease activity that carries out the actual strand breakage at the AP site left by a glycosylase. In other cases, it is left to the high pH to convert the AP site to a break.
(Unfortunately, as yet, there is no enzyme that recognizes bulky adducts. UvrABC is the bacterial enzyme complex that is potentially useful in this respect, but so far it has not been possible to use it on nucleoid DNA in gels.)
"FAQ by Andrew Collins, Gunnar Brunborg and Jonas Nygren, 2006, NewGeneris FP7-project"