In this study, we describe a new approach for studying protein–DNA interactions in solution. The approach is based on mapping the UV laser–induced protein–DNA cross-links between the amino acids of the protein and the DNA bases that are in direct contact. The approach was applied for studying the solution structure of the human necrosis factor (NF)–κB p50 homodimer bound to a 37 base pair DNA. Several points of contact identical to those observed in the NF-κB–DNA crystal structure were found between the two biomolecules. Evidence is provided for the occurrence of two new contact points, one for each DNA strand. These new points of contact are located symmetrically a base apart from the extremity of the binding sequence.
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Vol. 77 • No. 6