Effect O6‐guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations

Abstract

Alkylation of guanine at the O6 atom is a highly mutagenic DNA lesion because it alters the coding specificity of the base causing G:C to A:T transversion mutations. Specific DNA repair enzymes, e.g. O(6)-alkylguanin-DNA-Transferases (AGT), recognize and repair such damage after looping out the damaged base to transfer it into the enzyme active site. The exact mechanism how the repair enzyme identifies a damaged site within a large surplus of undamaged DNA is not fully understood. The O(6)-alkylation of guanine may change the deformability of DNA which may facilitate the initial binding of a repair enzyme at the damaged site. In order to characterize the effect of O(6)-methyl-guanine (O(6)-MeG) containing base pairs on the DNA deformability extensive comparative molecular dynamics (MD) simulations on duplex DNA with central G:C, O(6)-MeG:C or O(6)-MeG:T base pairs were performed. The simulations indicate significant differences in the helical deformability due to the presence of O(6)-MeG compared to regular undamaged DNA. This includes enhanced base pair opening, shear and stagger motions and alterations in the backbone fine structure caused in part by transient rupture of the base pairing at the damaged site and transient insertion of water molecules. It is likely that the increased opening motions of O(6)-MeG:C or O(6)-MeG:T base pairs play a decisive role for the induced fit recognition or for the looping out of the damaged base by repair enzymes.

Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions

“…All the production simulations were performed by employing the NAMD biomolecular simulation program . CHARMM36 all-atom parameters ,− were used for the B-DNA duplex and urea. The topology and parameters corresponding to the urea nucleotide were derived from the CHARMM Generalized Force Field (CGenFF) by combining urea, nucleotide, and amide parameters .…”

“…Although NMR experiments provide valuable information about the structures of urea- and formamide-incorporated B-DNA duplexes, the complete characterization of DNA duplexes with urea lesions has been difficult because of the resonance overlap of the signals. , Molecular dynamics (MD) simulations are, in general, very useful for studying the structure, dynamics, and thermodynamic stability of damaged and chemically modified nucleic acid duplexes. − In the study presented here, MD simulations have been performed on the B-DNA duplexes with a urea lesion opposite four nucleobases, adenine (A), thymine (T), guanine (G), and cytosine (C), in Watson–Crick (WC), Hoogsteen, and sugar edge interactions. Analyses of the MD trajectories suggest that the urea lesions prefer to form WC-like hydrogen bond interactions with the nucleobases, especially purines, and can potentially mimic the nucleobases in B-DNA duplexes.…”

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

“…Ab initio simulations have been used to compare the energetics of intact and mispaired Watson–Crick basepairs, demonstrating that selection of natural basepairs is primarily driven by hydrogen bonding and solvent interactions rather than stacking. A large number of MD studies have characterized the energetics involved in bending and flipping intact, damaged and mismatched bases of various sequences out of a DNA duplex, a topic that was previously reviewed . The simulations generally show that bases flip through the major groove, that the free energy cost of flipping is lower for mismatched bases compared with intact ones, and that the transition state is generally unfavorable, causing slow kinetics for switching between intrahelical and extrahelical states.…”