Iodine-125 radioprobing is based on incorporation of radioiodine into a defined position in a nucleic acid molecule. Decay of (125)I results in the emission of multiple, low-energy Auger electrons that, along with positively charged residual daughter nuclide, produce DNA strand breaks. The probability of such strand breaks at a given nucleotide is in inverse proportion to the distance from the (125)I atom to the sugar of that nucleotide. Therefore, conclusions can be drawn about the conformation or folding of a DNA or RNA molecule based on the distribution of (125)I decay-induced strand breaks. Here we describe in detail the application (125)I radioprobing for studying the conformation of quadruplex structures, and discuss the advantages and limitations of the method.