Influence of the Linkage Type and Functional Groups in the Carcinogenic Moiety on the Conformational Preferences of Damaged DNA: Structural and Energetic Characterization of Carbon- and Oxygen-Linked C⁸-Phenolic-Guanine Adducts

Abstract

Computational (DFT, MD, and free energy) methods are used to systematically compare the structural and energetic properties of C(8)-bonded 2'-deoxyguanosine (dG) adducts derived from phenolic toxins, namely, the oxygen-linked (unsubstituted) adduct ((PhO)dG) and carbon-linked adducts ((ortho-PhOH)dG or (para-PhOH)dG) that contain a hydroxyl group in the bulky moiety. Despite restricted rotation at the C(8)-X bond due to the presence of the oxygen linker, the (PhO)dG adduct likely possesses the greatest glycosidic (anti/syn) conformational flexibility at the 5'-terminus of DNA. However, the anti/syn energy difference is the smallest for the (para-PhOH)dG nucleotide at other helical positions, which correlates with the greatest conformational heterogeneity for the corresponding (NarI) adducted DNA. Most importantly, the total number of accessible conformations of adducted DNA depend on the phenolic adduct considered. Specifically, although the only conformations accessible to (PhO)dG adducted DNA correspond to the anti adduct glycosidic orientation, the C-linked adducts can also adopt the syn orientation in the double helix. Moreover, the number of accessible conformations for DNA containing the C-linked adducts depends on the nature of discrete interactions involving the hydroxyl group in the C(8)-moiety. In fact, such interactions lead to a novel (intercalated) conformational theme in the case of the (para-PhOH)dG adduct. Together, these results indicate that the type of C(8)-linkage, and the presence and location of additional functional groups in the bulky moiety affect the conformational outcomes, which adds to the list of previously established effects including the size of the carcinogenic moiety, adduct ionization state, and sequence context on the conformational preferences of damaged DNA. Most importantly, our study provides valuable structural information that explains the experimentally observed mutagenic potential of DNA phenolic adducts and predicts the relative repair propensity of the three phenolic lesions.

Chlorine Functionalization of a Model Phenolic C8-Guanine Adduct Increases Conformational Rigidity and Blocks Extension by a Y-Family DNA Polymerase

“…26 In this case, the Clinked adducts do not stabilize the SMI, but they have a strong syn-conformational preference (25−27 kJ mol −1 ). 26,27 Insertion of C opposite C-linked adducts requires the polymerase to flip the adduct from its stable syn-conformation into the energetically destabilized anti-conformation. The barrier for this process is proposed to cause polymerase stalling, an important aspect in the polymerase slippage mechanism.…”

“…The single-ringed N-linked C8-aniline-dG adduct preferentially induces B-type conformation and lacks potent mutagenicity. 25 In contrast to N-linked C8-dG adducts, C-linked lesions tend to induce B-type conformation, although conformational heterogeneity is observed depending on the size of the C8-aryl ring, 26 the nature and placement of substituents on the C8-aryl ring, 27 and the adduct ionization state. 28 Thus, C-and Nlinked adducts have different mutagenic outcomes.…”

Adduct Fluorescence as a Tool to Decipher Sequence Impact on Frameshift Mutations Mediated by a C-Linked C8-Biphenyl-Guanine Lesion

“…Our interest in C8-dG adducts has focused on the C- and O-linked analogs , in which a variety of C- and O-linked C8-dG adducts have been inserted into the G 3 position of Nar I to determine the impact of linkage type on adduct conformation and in vitro mutagenicity using primer extension assays. ,− Bulky O- and C-linked C8-dG adducts strongly stall primer extension by Kf – at the n + 1 site. The correct base C is mainly inserted opposite the lesion, along with small amounts of A. ,, In most instances, full-length extension products are not observed, and the GC dinucleotide deletion product has never been detected.…”

Understanding the Mutagenicity of O-Linked and C-Linked Guanine DNA Adducts: A Combined Experimental and Computational Approach

“…45,48 Initially, DFT (B3LYP/ 6-31G(d)) was used to map the conformational space of the nucleobase adduct to determine the intrinsic flexibility of the C8 linkage. 48 The most stable nucleobase structure is planar (Figure 3b) and exhibits significant flexibility, with the barriers for rotation about the bonds in the tether being less than 5−15 kJ mol −1 at the B3LYP/6-311+G(2df,p)//B3LYP/ 6-31G(d) level. Although the adduct remains planar about the linkage upon inclusion of 2′-deoxyribose, there is decreased flexibility about the bulky moiety−nucleobase bond for both the anti and syn glycosidic orientations of the nucleoside adduct due to steric interactions.…”

“…Structural information for the adducted NarI( 12) duplex with PhO-dG paired against complementary C was obtained from a rigorous sampling approach involving MD simulations initiated from multiple starting conformations based on the structural information obtained from DFT (i.e., the relative orientations of the bulky moiety with respect to the nucleobase and the nucleobase with respect to 2′-deoxyribose) and different possible positions of the bulky moiety in the DNA helix (i.e., minor groove, major groove, and intercalated; Figure 2). 48 When the adduct assumes the anti glycosidic orientation, a B-type duplex conformation is most stable (Table 1), with the bulky moiety in the major groove and solvent-exposed (Figure 4a). Although the bulky moiety typically resides in an orientation perpendicular to the nucleobase plane (Figure 4a), a reasonable degree of flexibility exists within the tether across the simulation trajectories.…”