Method and system for footprinting a nucleic acid molecule. A sample consists of a nucleic acid molecule in an environment in which --OH radicals are generated when the environment is irradiated with an X-ray beam having an intensity less than 10.sup.9 photons sec.sup.-1 mm.sup.-2 for an amount of time less than 1,000 msec. The sample is then irradiated with an X-ray beam having an intensity less than 10.sup.9 photons sec.sup.-1 mm.sup.-2 for an amount of time less than 1,000 msec so as to generate --OH radicals in the environment. Fragmentation of the nucleic acid molecule is then detected.