Mass Spectrometry Evidence for Forming Schiff Base 3′-DNA-Histone Cross-Links from Abasic Sites in Vitro and in Human Cells

Histones catalyze DNA strand incision at apurinic/apyrimidinic (AP) sites accompanied by the formation of reversible but long-lived DNA–protein cross-links at 3′-termini (3′-histone-DPCs). However, the chemical structures of 3′-histone-DPCs are not well characterized, and whether they are formed in cells is uncertain. In this study, we developed a liquid chromatography with tandem mass spectrometry workflow to characterize DPCs produced from the reaction of histones with AP sites and wish to report evidence that histones cross-link to incised AP sites via Schiff bases. We also demonstrated for the first time that 3′-histone-DPCs are produced endogenously in human embryonic kidney 293T cells.