Replication of the Aristolochic Acid I Adenine Adduct (ALI-N⁶-A) by a Model Translesion Synthesis DNA Polymerase: Structural Insights on the Induction of Transversion Mutations from Molecular Dynamics Simulations

Abstract

Exposure to aristolochic acid I and II (AAI and AAII) has been implicated in aristolochic acid nephropathy and urothelial carcinoma. The toxicological effects of AAs are attributed to their ability to form aristolacatam (AL)-purine DNA adducts. Among these lesions, the AL-adenine (ALI-N6-A and ALII-N6-A) adducts cause the “signature” A → T transversion mutations associated with AA genotoxicity. To provide the currently missing structural basis for the induction of these signature mutations, the present work uses classical all-atom molecular dynamics simulations to examine different (i.e., preinsertion, insertion, and postextension) stages of replication past the most abundant AA adduct (ALI-N6-A) by a representative lesion-bypass DNA polymerase (Dpo4). Our analysis reveals that, before dNTP incorporation (i.e., preinsertion step), ALI-N6-A adopts a nearly planar conformation at the N6-linkage and the ALI moiety intercalates within the DNA helix. Since this conformation occupies the dNTP binding site, the same planar lesion conformation results in a significant distortion of the polymerase active site at the insertion step and therefore replication will likely not be successful. However, if ALI-N6-A undergoes a small conformational change to introduce non-planarity at the N6-linkage during the insertion step, minimal distortion occurs in the Dpo4 active site upon incorporation of dATP. This insertion and subsequent extension would initially lead to A:A mismatches and then result in A → T transversion mutations during the second round of replication. In contrast, if a large conformation flip of the ALI moiety occurs at the insertion step to reorient the bulky moiety from an intercalated position into the major groove, dTTP (non-mutagenic) incorporation will be favored. Molecular dynamics (MD) simulations on postextension complexes reveal that damaged DNA will likely further rearrange during later replication steps to acquire a base-displaced intercalated conformation that is similar to that previously reported for (unbound) ALI-N6-A adducted DNA, with the exception of slight non-planarity at the lesion site. Overall, our results provide a structural explanation for both the successful non-mutagenic lesion bypass and the preferential misincorporation of dATP opposite ALI-N6-A and thereby rationalize the previously reported induction of A → T signature transversion mutations associated with AAs. This work should thereby inspire future biochemical experiments and modeling studies on the replication of this important class of DNA lesions by related human translesion synthesis polymerases.

Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch ykkC-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands

“…The electrostatic and van der Waals interaction energies obtained using the “lie” command were then added for each simulation frame considered to get the total interaction energies. In synchrony with previous studies, − only the nucleobase moieties were included for these calculations while excluding the sugar-phosphate backbone. However, the backbone was included for calculations in cases where the nucleotide sugar groups interacts with the ligand.…”

Translesion Synthesis across the N2-Ethyl-deoxyguanosine Adduct by Human PrimPol

“…MD trajectories were used to calculate various structural parameters associated with the insertion stage of replication. For successful replication, specific structural requirements are to be satisfied . These parameters are the optimal reaction distance (3.5 Å) between O3′–Pα of the primer and incoming nucleotide, the attack angle, O3′–Pα–Oαβ, of the primer and the incoming nucleotide (150°–180°), and the C1′–C1′ distance (10.8 Å) between the template and incoming nucleotides (Figure A).…”

“…For successful replication, specific structural requirements are to be satisfied. 63 These parameters are the optimal reaction distance (3.5 Å) between O3′−Pα of the primer and incoming nucleotide, the attack angle, O3′−Pα−Oαβ, of the primer and the incoming nucleotide (150°−180°), and the C1′−C1′ distance (10.8 Å) between the template and incoming nucleotides (Figure 6A). Along with these, a strong Watson crick base-pairing interaction between the incoming nucleotide and the template dG facilitates proper replication.…”

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

“…, A, C and G hydroxymethyl lesions) are particularly intriguing and experimental structural information is not available to rationalize such observations. 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.…”