Figure 1.

Basic premise of the CAFA approach. (A) DNA or RNA is exposed to a chemical or enzymatic probe that either cleaves or modifies it with single-hit kinetics such that the population of the reaction products (B) is related to the probe's reactivity. Extension of fluorescently labeled primers by RT or DNA polymerase generates a corresponding population of fluorescently labeled cDNA molecules (C). The cDNA samples are mixed with a Beckman size standard ladder (400 or 600). Each mixture is subject to CE yielding a trace of the size separated reaction products (D) to be analyzed by CAFA. The blue trace records the fluorescence emission of the Cy5 labeled cDNA fragments; the red peaks correspond to the Beckman WellRED® dye D1 present on the size standard fragments.