Figure 2. Identification of lysine residues involved in DNA binding.

(A) A typical MALDI-TOF spectrum of tryptic digests of XPA protein (left) or biotinylated XPA protein (right). Monoisotopic resolution for all of the peptide peaks were obtained, allowing unequivocal assignment of singly-charged unmodified and biotinylated peptide fragments. (B) the typical Q-TOF data illustrate the protection of a lysine residue in XPA. The peak corresponding to peptide fragment 221, 222, 224+biotin in XPA is an example of protection from modification by binding of ds–ssDNA junction DNA. When junction DNA is not present, K221, K222 and K224 is readily modified by NHS-biotin; however, in the presence of junction DNA the modification peak disappears. (C) in contrast, K188 is a lysine residue not protected by junction DNA binding. A modification peak appears upon treatment with NHS-biotin and persists following addition of junction DNA. Each multiply-charged peptide resulted in clearly resolved peak clusters, indicating monoisotopic resolution; unmodified peaks C1 and C2 serve as controls.