Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence

Abstract

2-Amino-3-methylimidazo[4,5-f]quinolone (IQ), a heterocyclic amine found in cooked meats, undergoes bioactivation to a nitrenium ion, which alkylates guanines at both the C8-dG and N2-dG positions. The conformation of a site-specific N2-dG-IQ adduct in an oligodeoxynucleotide duplex containing the iterated CG repeat restriction site of the NarI endonuclease has been determined. The IQ moiety intercalates, with the IQ H4a and CH3 protons facing the minor groove, and the IQ H7a, H8a and H9a protons facing the major groove. The adducted dG maintains the anti-conformation about the glycosyl bond. The complementary dC is extruded into the major groove. The duplex maintains its thermal stability, which is attributed to stacking between the IQ moiety and the 5′- and 3′-neighboring base pairs. This conformation is compared to that of the C8-dG-IQ adduct in the same sequence, which also formed a ‘base-displaced intercalated’ conformation. However, the C8-dG-IQ adopted the syn conformation placing the Watson−Crick edge of the modified dG into the major groove. In addition, the C8-dG-IQ adduct was oriented with the IQ CH3 group and H4a and H5a facing the major groove. These differences may lead to differential processing during DNA repair and replication.

Structural and energetic characterization of the major DNA adduct formed from the food mutagen ochratoxin A in the NarI hotspot sequence: influence of adduct ionization on the conformational preferences and implications for the NER propensity

“…Double-strand breaks can occur when a DNA lesion blocks replication by inhibiting the replication fork ( 84 ). Based on studies on other adducts, OTA replication blockage is likely caused by either a base-displaced intercalated structure that has evaded repair ( 48 ) or an intercalated structure formed at the template-primer junction ( 85 ). However, our calculated structures highlight the larger and more flexible amide-linked phenylalaninic moiety of OTB-dG in DNA compared to C8-substituents in other C8-dG adducts.…”

Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N2-dG DNA Adduct Positioned at the Nonreiterated G1 in the NarI Restriction Site

“…This result was similar to that observed for the N 2 -dG-IQ adduct located at position G 3 ( T m 63 °C) (Table S1, Supporting Information ). 64 …”

“…Partial charges for the modified base were calculated in GAUSSIAN 87 using the basis set B3LYP/6-31G*. 64 The starting structure was energy-minimized for 1000 cycles using the steepest descent method. The generalized Born model 88 with parameters developed by Tsui and Case 89 was used for implicit water simulation.…”

“…The conformation of the N 2 -dG-IQ adduct in this duplex, as determined by NMR spectroscopy, is similar to its conformation at the X 7 position (the G 3 position of the Nar I sequence). 64 The IQ heterocyclic ring forms a base-displaced intercalated conformation, disrupting Watson–Crick hydrogen bonding at the lesion site, and flips the complementary cytosine into the major groove. Thus, the N 2 -dG-IQ adduct favors a base-displaced intercalated conformation at both positions G 1 and G 3 of the Nar I sequence.…”

Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein

“…Different conformers of 2-(acetyl)aminofluorene-dG lesions have also been shown to play a role in their recognition and repair by NER [73][74] . While it is difficult to ascertain which conformation is prevalent in solution here for NPOM-DNA, base-displaced intercalated conformers can preferentially be stabilized in specific sequence contexts and be in equilibrium with major groove conformers [75][76][77] . Future studies are needed to reveal how Rad4binding changes the 3D structure of NPOM-DNA and how such structures impacts its repair by NER.…”