Biochemical Investigations into the Mutagenic Potential of 8-Oxo-2′-deoxyguanosine Using Nucleotide Analogues

Abstract

8-Oxo-2'-deoxyguanosine (OdG) is an abundant DNA lesion produced during oxidative damage to DNA. It can form relatively stable base pairs with both dC and dA that mimic natural dG:dC and dT:dA base pairs, respectively. Thus, when in the template strand, OdG can direct the insertion of either dCTP or dATP during replication, the latter of which can lead to a dG → T transversion. The potential for OdG to cause mutation is dependent on the preference for dCTP or dATP insertion opposite OdG, as well as the ability to extend past the resulting base pairs. The C2-amine and C8-oxygen could play major roles during these reactions since both would lie outside the Watson-Crick cognate base pairs shape in the major groove when OdG base pairs to dA and dC, respectively, and both have the ability to form strong interactions, like hydrogen bonds. To gain a more generalized understanding of how the C2-amine and C8-oxygen of OdG affect its mutagenic potential, the incorporation opposite and extension past seven analogues of dG/OdG that vary at C2 and/or C8 were characterized for three DNA polymerases, including an exonuclease-deficient version of the replicative polymerase from RB69 (RB69), human polymerase (pol) β, and polymerase IV from Sulfolobus solfataricus P2 (Dpo4). Based on the results from these studies, as well as those from previous studies with RB69, pol β, Dpo4, and two A-family polymerases, the influence of the C2-amine and C8-oxygen during each incorporation and extension reaction with each polymerase is discussed. In general, it appears that when the C2-amine and the C8-oxygen are in the minor groove, they allow OdG to retain interactions that are normally present during insertion and extension. However, when the two groups are in the major groove, they each tend to form novel active site interactions, both stabilizing and destabilizing, that are not present during insertion and extension with natural DNA.

Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes

“…DNA of all living beings is constantly affected by various factors such as highly reactive cell metabolites, ionizing radiation, ultraviolet rays, etc. Oxidized bases are the most common DNA damages, − which have always been associated with various types of cancers. , For example, a common oxidative damaged 7,8-dihydro-8-oxoguanine (8-oxo-G) can be mistaken for T and mismatch with normal base A in the process of DNA replication and then leads to GC → TA transversion. − In order to maintain the integrity of genetic information, a repair enzyme can recognize the oxidized base 8-oxo-G in a DNA double helix and then excise and repair the oxidized DNA. , The key step is to accurately recognize the oxidized base by the enzyme. However, the microscopic mechanism of recognization is currently not clear.…”

Insights into the substrate specificity of the MutT pyrophosphohydrolase using structural analogues of 8-oxo-2′-deoxyguanosine nucleotide

“…Previously, we have used OdG analogues to establish structure-activity relationships of OdG with repair enzymes and various polymerases. 22–24 In this study, nine OdGTP analogues were used to investigate the contribution of three sites to MutT activity. Those sites include i) C8, where a large atom can promote the syn N -glycosidic bond conformation 5, 25 that is observed in the active site of the binary MutT:OdGMP structure, ii) N7, where the presence of a hydrogen can lead to a stabilizing interaction with Asn119, and iii) C2, where the exocyclic amine can form both a direct hydrogen bond with the main chain carbonyl of Phe35 and a water-mediated hydrogen bond with the main chain carbonyl of Gly37 (Fig.…”