Accommodation of an <i>N</i>-(Deoxyguanosin-8-yl)-2-acetylaminofluorene Adduct in the Active Site of Human DNA Polymerase ι: Hoogsteen or Watson−Crick Base Pairing?

Donny-Clark, Kerry; Shapiro, Robert; Broyde, Suse

doi:10.1021/bi801283d

Cited by 19 publications

(22 citation statements)

References 96 publications

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“…The APG base and DNA backbone are shifted out toward the major groove to achieve a standard C1′–C1′ distance for anti -guanine:dCTP Watson–Crick base pairing (Figure 2C and 3A). This observation is consistent with the prediction that Watson–Crick base pairing could occur in the polι active site for a major groove adduct by a previous modeling study (37). Thus, our APG-dCTP structure illustrates how polι can accommodate the APG lesion in Watson–Crick base pairing, a mechanism different from Hoogsteen base pairing observed in all the previous purine template structures of polι (33).…”

Section: Resultssupporting

confidence: 93%

Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase

Kirouac

Basu

2012

Nucleic Acids Research

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Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyrene–derived DNA lesions generates mutations that likely play a role in the etiology of cancer. Here, we report two crystal structures of the human Y-family DNA polymerase iota complexed with the major 1-nitropyrene DNA lesion at the insertion stage, incorporating either dCTP or dATP nucleotide opposite the lesion. Polι maintains the adduct in its active site in two distinct conformations. dCTP forms a Watson–Crick base pair with the adducted guanine and excludes the pyrene ring from the helical DNA, which inhibits replication beyond the lesion. By contrast, the mismatched dATP stacks above the pyrene ring that is intercalated in the helix and achieves a productive conformation for misincorporation. The intra-helical bulky pyrene mimics a base pair in the active site and facilitates adenine misincorporation. By structure-based mutagenesis, we show that the restrictive active site of human polη prevents the intra-helical conformation and A-base misinsertions. This work provides one of the molecular mechanisms for G to T transversions, a signature mutation in human lung cancer.

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Section: Resultssupporting

confidence: 93%

Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase

Kirouac

Basu

2012

Nucleic Acids Research

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“…18,38,39 The resulting SMI is stabilized by various chemical interactions within the binding pocket and will hinder translocation during TLS. 18,36,56 For example, Schorr and Carell 41 showed that frameshift formation is triggered by the unstable base pairing of the AAF lesion with the correct incoming dC. Such configurations have been observed in replicative and bypass polymerases.…”

Section: Discussionmentioning

confidence: 99%

“…Such configurations have been observed in replicative and bypass polymerases. 18,38,39,56 To this end, we reported the structures of the FAAF-modified Nar I-sequence corresponding to −1, −2, and −3 deletion duplexes. 33 These SMIs exist in a mixture of B- and S-SMI conformers, with the population of the S conformer and the thermodynamic stability being in the order of −1 > −2 > −3.…”

Section: Discussionmentioning

confidence: 99%

Conformational Insights into the Mechanism of Acetylaminofluorene-dG-Induced Frameshift Mutations in the NarI Mutational Hotspot

Cho

2016

Chem. Res. Toxicol.

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Frameshift mutagenesis encompasses the gain or loss of DNA base pairs, resulting in altered genetic outcomes. The NarI restriction site sequence 5'-G1G2CG3CX-3' in Escherichia coli is a well-known mutational hotspot, in which lesioning of acetylaminofluorene (AAF) at G3* induces a greater -2 deletion frequency than that at other guanine sites. Its mutational efficiency is modulated by the nature of the nucleotide in the X position (C ∼ A > G ≫ T). Here, we conducted a series of polymerase-free solution experiments that examine the conformational and thermodynamic basis underlying the propensity of adducted G3 to form a slipped mutagenic intermediate (SMI) and its sequence dependence during translesion synthesis (TLS). Instability of the AAF-dG3:dC pair at the replication fork promoted slippage to form a G*C bulge-out SMI structure, consisting of S- ("lesion stacked") and B-SMI ("lesion exposed") conformations, with conformational rigidity increasing as a function of primer elongation. We found greater stability of the S- compared to the B-SMI conformer throughout TLS. The dependence of their population ratios was determined by the 3'-next flanking base X at fully elongated bulge structures, with 59% B/41% S and 86% B/14% S for the dC and dT series, respectively. These results indicate the importance of direct interactions of the hydrophobic AAF lesion with the 3'-next flanking base pair and its stacking fit within the -2 bulge structure. A detailed conformational understanding of the SMI structures and their sequence dependence may provide a useful model for DNA polymerase complexes.

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“…1c). Although this “wedge” W-conformer led to severe distortion of the DNA binding area in the active site of Pol iota (12), it is a distinct possibility in polymerase-free duplex DNA (13). …”

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confidence: 99%

Structures of 2-Acetylaminofluorene Modified DNA Revisited: Insight into Conformational Heterogeneity

Patnaik

Cho

2010

Chem. Res. Toxicol.

103

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Despite the extensive data on dG-AAF, the major DNA adduct derived from the model carcinogen 2-acetylaminofluorene, little is known with respect to its solution structures. Here we provide NMR/CD evidence for three conformers of dG-AAF in duplex DNA: major groove (B), basedisplaced stacked (S), and minor groove wedge (W). The S/B/W-conformational heterogeneities were found to be sensitive to the nature of the flanking DNA sequence contexts and pH.Arylamines and their nitro derivatives are a major group of environmental mutagens, and have been implicated in the etiology of human cancers (1). In vivo metabolic activation of the prototype carcinogens 2-acetylaminofluorene (2) and 2-nitrofluorene (3) results in production of dG-AF1 and dG-AAF as major stable adducts (Fig. 1a) (4). Despite their structural similarities, the two DNA adducts exhibit distinct mutation and repair activities. dG-AF has been shown to adopt multiple conformers, giving rise to unique sequencedependent mutation and repair outcomes (5,6). However, very little is known about the structure-function relationships of dG-AAF, which is remarkable given the extensive in vivo and in vitro data that have accumulated related to AAF (3,277 items on PubMed Search for "acetylaminofluorene").In 1993, O'Handley et al. (7) reported that ~70% of an AAF-modified 9-mer duplex in the CG[AAF]C sequence context adopts a base-displaced S-conformer with stacking of the fluorene moiety into a double helix (Fig. 1c). The structure of the remaining 30% of the AAF-modified duplex has not been elucidated. Using an 19 F NMR approach (8), we showed that a 12-mer duplex in the TG*A sequence context (Duplex II, G*=FAAF, Fig. 1b) exhibits 40:60% 19 F signals with an exclusive presence of the S-conformer, differing only in the Nacetyl group's cis and trans conformation (9). This result contrasts with data from AF and FAF (Fig. 1a), which consistently adopt an S/B conformational heterogeneity (6,10).We here present new data that provides further insights on the conformers that contribute to the conformational mix of dG-AAF in solution. Specifically, our results are consistent with adoption by dG-AAF of a major groove B-type (B) and a minor groove "wedge" (W) conformer, in addition to the S-conformer elucidated by O'Handley et al. (7) (Fig. 1c), and that sequence context determines the population balance between the states. The B-type conformer has a glycosyl bond conformation that is anti, while S and W are syn. The (11) and Pol iota (12). As observed in the S-conformer, the AAF-modified dG adopts the syn conformation; however, instead of having disrupted hydrogen bonding, the modified dG can pair with the complementary dC utilizing its Hoogsteen edge; this places the acetylamino moiety in the narrow minor groove (13) (Fig. 1c). Although this "wedge" W-conformer led to severe distortion of the DNA binding area in the active site of Pol iota (12), it is a distinct possibility in polymerase-free duplex DNA (13). NIH Public AccessIn the present study, we conducted spectr...

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Accommodation of an N-(Deoxyguanosin-8-yl)-2-acetylaminofluorene Adduct in the Active Site of Human DNA Polymerase ι: Hoogsteen or Watson−Crick Base Pairing?

Cited by 19 publications

References 96 publications

Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase

Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase

Conformational Insights into the Mechanism of Acetylaminofluorene-dG-Induced Frameshift Mutations in the NarI Mutational Hotspot

Structures of 2-Acetylaminofluorene Modified DNA Revisited: Insight into Conformational Heterogeneity

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