Computational Study of the Formation of C8, C5, and C4 Guanine:Lysine Adducts via Oxidation of Guanine by Sulfate Radical Anion
journal contributionposted on 2019-05-29, 00:00 authored by Bishnu Thapa, Sebastien P. Hebert, Barbara H. Munk, Cynthia J. Burrows, H. Bernhard Schlegel
Oxidative damage to DNA can lead to DNA–protein cross-links which can interfere with DNA transcription, replication, and repair. In experimental studies modeling oxidative damage to DNA, oxidation of guanosine by sulfate radical anion in the presence of lysine produced a mixture of lysine (Lys)-substituted spiroiminodihydantoins (Sp): ∼65% 5-Lys-Sp, ∼30% 8-Lys-Sp, and ∼5% 5,8-diLys-Sp. Pathways for formation of the lysine adducts during the oxidation of guanine by sulfate radical anions have been mapped out using B3LYP density functional theory and the SMD solvation model. Methylamine was used as a model for lysine, and imidazole served as a proton acceptor. The lowest barrier for methylamine reaction with guanine radical is addition at C8, yielding mainly 8-NHR-Sp and some 5,8-diNR-Sp. This is in good agreement with the cross-link ratios for mild oxidations mediated by type I photosensitizers such as benzophenone, but this is not in agreement with the product ratios for strong oxidants such as sulfate radical anion. The calculations explored pathways for oxidation of guanine by sulfate radical anion that produced guanine radical and radical cation and doubly oxidized guanine (Gox) and its cation. Sulfate radical anion can also oxidize methylamine to produce neutral methylamine radical (CH3NH•) after deprotonation. The calculations qualitatively reproduced the observed product ratio at pH 7 via a pathway involving the barrierless addition of methylamine radical at C5 and C8 of guanine radical. After C5 addition of methylamine radical, the lowest barrier is for H2O addition at C8 leading exclusively to 5-NHR-Sp. After C8 addition of methylamine radical, H2O and methylamine addition to C5 lead to 8-NHR-Sp and some 5,8-diNR-Sp.