Evidence for multiple imino intermediates and identification of reactive nucleophiles in peptide-catalyzed beta-elimination at abasic sites.
Prior investigations have demonstrated that peptides containing a single aromatic residue flanked by basic ones, such as Lys-Trp-Lys, can incise the phosphodiester backbone of duplex DNA at an AP site via beta-elimination. An amine serves as the reactive nucleophile to attack C1' on the ring-open deoxyribose sugar to form a transient peptide-DNA imino (Schiff base) intermediate, which may be isolated as a stable covalent species under reducing conditions. In the current study, we use this methodology to demonstrate that peptide-catalyzed beta-elimination proceeds via the formation of two Schiff base intermediates, one of which was covalently trapped prior to strand incision and the other following strand incision. N-Terminal acetylation of reactive peptides significantly inhibited formation of a trapped Schiff base complex; thus, we demonstrate for the first time that the preferred reactive nucleophile for peptides catalyzing strand incision is the N-terminal alpha-amino group, not an epsilon-amino group located on a lysine residue as previously postulated. Trapping reactions in which the central tryptophan residue was changed to alanine did not have a significant impact on the efficiency of Schiff base formation, indicating that the presence of an aromatic residue is dispensable for the step prior to peptide-catalyzed beta-elimination. Interestingly, the methodology presented here affords a convenient means for covalently attaching an array of peptides onto AP site-containing DNA in a site-specific fashion. We suggest that the generation of such DNA-peptide cross-links may provide utility in studying the repair of biologically significant DNA-protein cross-link damage as DNA-peptide complexes may mimic intermediate structures along a repair pathway for DNA-protein cross-links.
Kurtz
Andrew J
AJ
Sealy Center for Molecular Science and Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas 77555-1071, USA.
Dodson
M L
ML
Lloyd
R Stephen
RS
D024322:Amino Acids, Aromatic / Q000737:chemistry*; D019757:Carbon-Oxygen Lyases / Q000502:physiology; D003432:Cross-Linking Reagents / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D045647:DNA Glycosylases; D004277:DNA, Single-Stranded / Q000737:chemistry; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase; D003855:Deoxyribose / Q000737:chemistry; D008239:Lysine / Q000737:chemistry*; D009699:N-Glycosyl Hydrolases / Q000502:physiology; D009842:Oligopeptides / Q000737:chemistry*; D012545:Schiff Bases / Q000737:chemistry*; D012964:Sodium / Q000737:chemistry
D024322:Amino Acids, Aromatic; D003432:Cross-Linking Reagents; D004277:DNA, Single-Stranded; D009842:Oligopeptides; D012545:Schiff Bases; D003855:Deoxyribose; D004247:DNA; D012964:Sodium; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; D019757:Carbon-Oxygen Lyases; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase; D008239:Lysine