Molecular Dynamics Study of One-Base Deletion Duplexes Containing the Major DNA Adduct Formed by Ochratoxin A: Effects of Sequence Context and Adduct Ionization State on Lesion Site Structure and Mutagenicity

Abstract

Ochratoxin A (OTA) is a ubiquitous food toxin associated with chronic nephropathy in humans and renal carcinogenicity in rodents. The mutational spectra of cells exposed to OTA reveal that one-base deletions comprise the largest percentage (73%) of the total mutations that occur upon OTA exposure. To contribute toward understanding the prevalence of OTA-induced one-base deletion mutations, the present work uses molecular dynamics (MD) simulations to analyze the conformational preferences of one-base deletion duplexes containing OT-G, the major OTA adduct (addition product) at the C8-site of guanine. Specifically, the influence of OT-G in four possible ionization states and three sequence contexts (G1, G2 and G3 in the NarI (5′–G1G2CG3CC–3′), a prokaryotic mutational hotspot sequence) on the structure of the adducted DNA is investigated. Our data reveal that the damaged helices are stable in two (B-type (B) and stacked (S)) conformations that are structurally similar to those adopted by common N-linked C8-guanine lesions. However, the adduct ionization state and sequence context affect the degree of helical distortion and the B/S conformational heterogeneity, which will impact the lesion repair and replication outcomes. This finding correlates with the experimentally reported tissue-specific mutagenicity of OTA exposure. Furthermore, regardless of the adduct conformation, ionization state, or sequence context, more stable lesion-site interactions and lack of disruption of the flanking base pairs in the one-base deletion duplexes compared to the corresponding two-base deletion helices rationalize the greater abundance of OTA induced one-base deletions. Overall, our work provides valuable structural insights that help explain the experimentally observed mutagenicity associated with OTA.

Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond

“…Scheme 1 ) are very small and positioned around RMSF values 1.17 ± 0.24, 1.74 ± 0.29, and 1.69 ± 0.29 Å, respectively. We may thus conclude that, in accordance with previous studies of DNA oligonucleotides, 56 1 μs simulations ensure convergence of key DNA structural parameters, and reliable conclusions can be drawn.…”

“…Furthermore, the standard deviation in the RMSD over the last 0.1 μs simulation is only 0.40 Å (Figure a), showing that the relative structural change is very small. Therefore, in accordance with previous studies of natural and damaged DNA, detailed structural analysis was carried out on the last 0.1 μs simulation. In addition, root-mean-square fluctuation (RMSF) values were calculated to investigate how much the individual nucleobases moved during the simulations .…”

Establishing Linkages Among DNA Damage, Mutagenesis, and Genetic Diseases

“…193,197−202 Even so, a combination of structural (NMR and crystal structure analyses) and computation studies carried out by Geacintov, Patel, Stone, Broyde, Wetmore and others has provided much needed links between the structure and conformation of a lesion in different sequences and the biological effects of that lesion. 51,192,202,203 There are only two studies in which context-dependent repair and replication have been studied in all three-base contexts. Delaney and Essigmann constructed a panel of 16 phage genomes in which O 6 -mG was placed in each of the 16 possible three-base contexts (e.g., 5′-NXN-3′, where X is O 6 -mG and N is any base).…”

“…Nucleotide excision repair susceptibility of the (+)- trans-anti -[BP]- N 2 -dG adduct in several sequences shows that dynamic periodic denaturation of Watson–Crick base pairing on the 5′ flank of the lesion provides a strong recognition signal for repair in these sequences. , Biophysical studies showing marked local thermodynamic destabilization are consistent with this notion. Mutagenesis of the (+)- trans-anti -[BP]- N 2 -dG adduct also is context dependent. , Mutagenesis of the oxidative DNA damages 8-OxoG and Fapy·dG in human cells is also strongly dependent on DNA sequence context. , However, these and similar studies with other DNA lesions have been carried out in a limited number of DNA sequences. ,− Even so, a combination of structural (NMR and crystal structure analyses) and computation studies carried out by Geacintov, Patel, Stone, Broyde, Wetmore and others has provided much needed links between the structure and conformation of a lesion in different sequences and the biological effects of that lesion. ,,, …”

Multiscale computational investigations of the translesion synthesis bypass of tobacco-derived DNA adducts: critical insights that complement experimental biochemical studies

“…Nevertheless, computational chemistry has proven to be an effective tool to complement experimental studies for a wide range of lesions, 69 including those arising from AAs, 6,70,71 PAH, 6,70,72–74 aristolochic acids, 75–78 phenols, 79–82 and ochratoxin A. 83–87 This perspective further highlights the unique role computational chemistry can play in deciphering the mutagenicity of DNA adducts by concentrating on tobacco-derived DNA lesions with varying sizes, flexibilities, parent nucleobases, and damage positions. Specifically, the usefulness of computational approaches and models that systematically vary in scale and complexity is emphasized.…”