Computational Study of the Formation of C8, C5, and C4 Guanine:Lysine Adducts via Oxidation of Guanine by Sulfate Radical Anion

Abstract

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 (G ox ) and its cation. Sulfate radical anion can also oxidize methylamine to produce neutral methylamine radical (CH 3 NH • ) 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 H 2 O addition at C8 leading exclusively to 5-NHR-Sp. After C8 addition of methylamine radical, H 2 O and methylamine addition to C5 lead to 8-NHR-Sp and some 5,8-diNR-Sp.

Computational Study of the Oxidation of Guanine To Form 5-Carboxyamido-5-formamido-2-iminohydantoin (2Ih)

“…2 This can be explained by the lower barrier for C8 addition of water to guanine radical cation compared to C5 addition. 51 Ghude et al found that guanine oxidation, in the presence of Ni (II) coordinated with a tetraazamacrocycle (NiCR) and KHSO 5 , results in 2Ih as the predominant, and in some cases exclusive, oxidation product of guanine. 48 This was proposed to be due to coordination of the nickel complex with guanine, potentially favoring the C5 center for nucleophilic addition over the C8 center.…”

“…In the absence of bicarbonate, sulfate radicals can oxidize guanine directly, resulting in 8oxoG under acidic conditions but no 2Ih . This can be explained by the lower barrier for C8 addition of water to guanine radical cation compared to C5 addition . Ghude et al found that guanine oxidation, in the presence of Ni (II) coordinated with a tetraazamacrocycle (NiCR) and KHSO 5 , results in 2Ih as the predominant, and in some cases exclusive, oxidation product of guanine .…”

“…While many studies have found 2Ih, − ,,− the mechanistic pathways for its formation are not well understood. In previous studies, we have used density functional calculations to explore mechanisms for guanine oxidation to form 8oxoG, Sp, Gh, and FAPyG, − formation of guanine-lysine cross-links mediated by type I and type II photosensitizers , and by sulfate radical, and formation of guanine-thymine cross-link products . We have also calculated p K a s and reduction potentials for nucleobases and intermediates in the guanine oxidation mechanism. − In this computational study, we address pathways leading to 2Ih.…”

Reaction Kinetics, Product Branching, and Potential Energy Surfaces of 1O2-Induced 9-Methylguanine–Lysine Cross-Linking: A Combined Mass Spectrometry, Spectroscopy, and Computational Study

“…There is no obvious saddle point, which leads to the formation of 5-LysNH 2 + –9MSp from 5-LysNH 2 + –9MOG. The studies of Schlegel et al on guanine–lysine adduct formation also found that acyl migration requires anionic states (and in a few cases, neutrals). , The reaction barrier TS4 for 9MOG OX + LysNH 3 + is comparable to TS3a and TS3b but lower than TS3c; the latter is the barrier leading to the formation of gem -9Mdiol. These calculation results are consistent with the experimental finding that the product branching ratio for cross-links (path 2b) is slightly higher than that for path 2a ( gem -9Mdiol + 9MGh, see Figure a).…”

“…Burrows and co-workers have examined the H 2 O-, NH 3 -, and lysine adducts of the oxidized guanine in nucleosides and single- and double-stranded oligodeoxynucleotides. , They reported different DPC structures depending on the nature of oxidants, e.g., 1 O 2 , lysine radicals, Na 2 IrCl 6 , or sulfate radicals. Accompanying the experimental work, Schlegel and co-workers have explored the 1 O 2 - and radical-mediated reaction pathways and intermediates for guanine–lysine cross-linking using various electronic structure calculations. ,, More recently, Dumont and co-workers have probed guanine–lysine cross-links using molecular dynamics simulations. , The 1 O 2 -specific guanine–lysine cross-linking mechanism may be summarized by Path 2b (highlighted in blue in Scheme ). That is, the presence of lysine during the 1 O 2 oxidation of G produces C5-lysine-substituted spiroiminodihydantion 5-LysNH-Sp exclusively. , …”