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. Author manuscript; available in PMC: 2009 Aug 27.
Published in final edited form as: Methods Mol Biol. 2009;543:403–437. doi: 10.1007/978-1-60327-015-1_25

Figure 1.

Figure 1

Site-specific protein-DNA photocrosslinking (1–6). (A,B) Chemical and enzymatic reactions are used to prepare a full-length-promoter DNA fragment with a phenyl-azide photoactivatible crosslinking agent (R) and an adjacent radioactive phosphorus (*) incorporated at a single, defined site. Based on the chemistry of incorporation, the maximum distance between the site of incorporation and the photoreactive atom is 9.7 Å; the maximum distance between the site of incorporation and a crosslinked atom is ~11 Å. (C) UV-irradiation of the derivatized protein-DNA complex initiates crosslinking. Nuclease digestion eliminates uncrosslinked DNA and converts crosslinked, radiolabelled DNA to a crosslinked, radiolabelled 3–5 nucleotide “tag.”