Effect of base sequence context on the conformational heterogeneity of aristolactam-I adducted DNA: structural and energetic insights into sequence-dependent repair and mutagenicity

Abstract

Aristolochic acids (AAs) are nephrotoxic and potentially carcinogenic plant mutagens that form bulky DNA adducts at the exocyclic amino groups of the purines. The present work utilizes classical molecular dynamics simulations and free energy calculations to investigate the role of lesion site sequence context in dictating the conformational outcomes of DNA containing ALI-N-dA, the most persistent and mutagenic adduct arising from the AAs. Our calculations reveal that the base-displaced intercalated conformer is the lowest energy conformer of damaged DNA in all sequence contexts considered (CXC, CXG, GXC and GXG). However, the experimentally-observed greater mutagenicity of the adduct in the CXG sequence context does not correlate with the relative thermodynamic stability of the adduct in different sequences. Instead, AL-N-dA adducted DNA is least distorted in the CXG sequence context, which points toward a possible differential repair propensity of the lesion in different sequences. Nevertheless, the structural deviations between adducted DNA with different lesion site sequences are small, and therefore other factors (such as interactions between the adducted DNA and lesion-bypass polymerases during replication) are likely more important for dictating the observed sequence-dependent mutagenicity of ALI-N-dA.

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

“…This postextension complex will eventually result in the base-displaced intercalated conformation of (unbound) damaged DNA previously reported in the literature. 13,51,52,54 However, future studies are required to examine the feasibility of the conformational flip of the base opposing the lesion from the intrahelical orientation to the extrahelical orientation and thereby confirm the hypothesis put forward in the present work.…”

“…Similar to the planar intercalated conformation, anti dCTP, anti dTTP, anti dATP, syn dATP, anti dGTP, or syn dGTP were reiteratively incorporated opposite the lesion in six independent MD simulations. Despite considering multiple initial (intercalated or major groove) adduct orientations for the postextension step, only an intercalated conformation analogous to the conformation adopted by ALI-N 6 -dA adducted DNA helices 13,51,52,54 was stable during the simulations, with the exception of non-planarity at the N 6 linkage. In postextension complexes, the adduct was reiteratively paired opposite all the anti canonical nucleosides (four independent simulations) and the two syn purine nucleosides in six independent simulations.…”

“…Regardless, the first 10 ns of each simulation were discarded as the equilibration phase and the final analysis was carried out on the last 90 ns of the total production run. The cpptraj and ptraj modules of AMBER 14 54 were used to analyze the backbone rmsd, average interatomic distances, angles, dihedral angles, and hydrogen-bonding occupancies. The hydrogen-bonding occupancies were determined by imposing a cutoff value of 3.4 Å for the donor−acceptor distance and 120°for the donor− hydrogen−acceptor angle, using the "hbond" command of cpptraj.…”

“…With the exception of the polymerase-induced nonplanarity within the ALI-N 6 -A adduct, this postextension conformation is similar to the structure deduced in previous computational studies on isolated DNA adduct containing the ALI-N 6 -A adduct. 13,51,52,54 This in turn indicates that, after lesion bypass, the lesion will adopt an intrahelical conformation regardless of whether the intercalated or major groove conformation exists at the insertion step and the base opposing the lesion may also undergo realignment from an intercalated conformation to an extrahelical orientation when damaged DNA is still bound to the polymerase. This postextension complex will eventually result in the base-displaced intercalated conformation of (unbound) damaged DNA previously reported in the literature.…”

“…Each complex was neutralized using five sodium ions and solvated in a truncated octahedral box of TIP3P water molecules, such that each atom in the complex was at least 8 Å away from the edge of the box in all directions. Parameters for the bonded terms of the force field of natural DNA nucleotides were modeled using ff14SB, while these parameters for ALI-N 6 -A , and the dNTPs , were adopted from previous studies. The Mg 2+ ions were described using the Allnér et al parameters, whereas Na + ions were simulated using Joung and Cheatham’s ion parameters .…”