Abstract: The present invention provides methods for the detection and quantitation of any modification of interest in any nucleic acid sequence. In particular, the invention provides methods for detecting and quantitating low levels of modifications of interest in DNA sequences. The methods of the invention take advantage of combining the use of nucleic acid sequence modification-specific molecules which are specific for DNA modifications, of fluorescently labelled proteins which are specific for the nucleic acid sequence modification-specific molecules, of capillary electrophoresis and of laser-induced fluorescence. The methods of the invention are useful for identifying and detecting exposure to carcinogens, in early risk assessment for cancer, and in monitoring of cancer therapy.