Fig. 2.

A schematic outline of synchrotron x-ray •OH footprinting. X-ray radiolysis of water produces •OH that diffuses to a fragment of labeled duplex DNA to allow detection of a unique set of cleavage products. Cleavage by •OH is relatively uniform under single-hit conditions, yielding a series of bands representing molecules with n, n + 1, n + 2... nucleotides that are sized by gel electrophoresis. Protein binding to specific DNA sequences protects the backbone of these nucleotides from •OH cleavage, resulting in decreased density of the electrophoretic bands corresponding to these nucleotides.