Rationale for Hydroxyl Radicals as a Probe

The hydroxyl radical is a small, highly reactive probe that is formed in water and primarily targets hydrophobic residues [109]. This may be an ideal probe for protein-protein interactions because tyrosine, tryptophan and phenylalanine are most likely to be found at an interface [110, 111]. Although protein-DNA interfaces are comprised of charged and hydrogen-bond donor side-chains, even these residues may be probed by hydroxyl radicals [112]. 

The hydroxyl radical reacts at nearly a diffusion limited rate (k 1 x 10 s to 5 X 10 s ) with the aromatic amino acids, as well as with me- 

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