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Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence.

Jain V, Hilton B, Patnaik S, Zou Y, Chiarelli MP, Cho BP - Nucleic Acids Res. (2012)

Bottom Line: Our (19)F-NMR/ICD results showed that FAAF at G(1) and G(3) prefer syn S- and W-conformers, whereas anti B-conformer was predominant for G(2).The melting and thermodynamic data indicate that the S- and W-conformers produce greater DNA distortion and thermodynamic destabilization.The present results provide valuable conformational insight into the sequence-dependent UvrABC incisions of the bulky aminofluorene DNA adducts.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA.

ABSTRACT
Nucleotide excision repair (NER) is a major repair pathway that recognizes and corrects various lesions in cellular DNA. We hypothesize that damage recognition is an initial step in NER that senses conformational anomalies in the DNA caused by lesions. We prepared three DNA duplexes containing the carcinogen adduct N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene (FAAF) at G(1), G(2) or G(3) of NarI sequence (5'-CCG(1)G(2)CG(3)CC-3'). Our (19)F-NMR/ICD results showed that FAAF at G(1) and G(3) prefer syn S- and W-conformers, whereas anti B-conformer was predominant for G(2). We found that the repair of FAAF occurs in a conformation-specific manner, i.e. the highly S/W-conformeric G(3) and -G(1) duplexes incised more efficiently than the B-type G(2) duplex (G(3)∼G(1)> G(2)). The melting and thermodynamic data indicate that the S- and W-conformers produce greater DNA distortion and thermodynamic destabilization. The N-deacetylated N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (FAF) adducts in the same NarI sequence are repaired 2- to 3-fold less than FAAF: however, the incision efficiency was in order of G(2)∼G(1)> G(3), a reverse trend of the FAAF case. We have envisioned the so-called N-acetyl factor as it could raise conformational barriers of FAAF versus FAF. The present results provide valuable conformational insight into the sequence-dependent UvrABC incisions of the bulky aminofluorene DNA adducts.

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Related in: MedlinePlus

(a) CD spectral overlays recorded at 15°C and (b) DSC curves recorded in 20 mM phosphate buffer containing 0.1 M NaCl at pH 7.0 of fully paired 16-mer NarI duplexes with FAAF modification at G1 (green), G2 (blue) and G3 (pink).
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gkr1307-F3: (a) CD spectral overlays recorded at 15°C and (b) DSC curves recorded in 20 mM phosphate buffer containing 0.1 M NaCl at pH 7.0 of fully paired 16-mer NarI duplexes with FAAF modification at G1 (green), G2 (blue) and G3 (pink).

Mentions: Figure 3a shows an overlay of the CD spectra for the three FAAF-modified NarI–G1, –G2 and –G3 duplexes relative to the unmodified control (red). Unmodified and FAAF-adducted duplexes both displayed a positive and negative ellipticity at around 270 and 250 nm, respectively, which is an S-curve characteristic of a B-form DNA double helix. The modified duplexes displayed significant blue shifts relative to the unmodified duplex, NarI–G3 (6 nm) >> NarI–G1 ∼ G2 (3 nm), indicating adduct-induced DNA bending. A concomitant increase in the positive intensity around 270 nm was noted in the order of G3 ∼ G1 > G2, which could be due to the interaction of the intercalated S-conformeric FAAF with neighboring bases. We noted a similar blue shift and hyperchromic effect for the highly (75%) S-conformeric FAF-modified NarI–G3 duplex (Figure 3b and Table 1 in Ref. 20).Figure 3.


Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence.

Jain V, Hilton B, Patnaik S, Zou Y, Chiarelli MP, Cho BP - Nucleic Acids Res. (2012)

(a) CD spectral overlays recorded at 15°C and (b) DSC curves recorded in 20 mM phosphate buffer containing 0.1 M NaCl at pH 7.0 of fully paired 16-mer NarI duplexes with FAAF modification at G1 (green), G2 (blue) and G3 (pink).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351159&req=5

gkr1307-F3: (a) CD spectral overlays recorded at 15°C and (b) DSC curves recorded in 20 mM phosphate buffer containing 0.1 M NaCl at pH 7.0 of fully paired 16-mer NarI duplexes with FAAF modification at G1 (green), G2 (blue) and G3 (pink).
Mentions: Figure 3a shows an overlay of the CD spectra for the three FAAF-modified NarI–G1, –G2 and –G3 duplexes relative to the unmodified control (red). Unmodified and FAAF-adducted duplexes both displayed a positive and negative ellipticity at around 270 and 250 nm, respectively, which is an S-curve characteristic of a B-form DNA double helix. The modified duplexes displayed significant blue shifts relative to the unmodified duplex, NarI–G3 (6 nm) >> NarI–G1 ∼ G2 (3 nm), indicating adduct-induced DNA bending. A concomitant increase in the positive intensity around 270 nm was noted in the order of G3 ∼ G1 > G2, which could be due to the interaction of the intercalated S-conformeric FAAF with neighboring bases. We noted a similar blue shift and hyperchromic effect for the highly (75%) S-conformeric FAF-modified NarI–G3 duplex (Figure 3b and Table 1 in Ref. 20).Figure 3.

Bottom Line: Our (19)F-NMR/ICD results showed that FAAF at G(1) and G(3) prefer syn S- and W-conformers, whereas anti B-conformer was predominant for G(2).The melting and thermodynamic data indicate that the S- and W-conformers produce greater DNA distortion and thermodynamic destabilization.The present results provide valuable conformational insight into the sequence-dependent UvrABC incisions of the bulky aminofluorene DNA adducts.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA.

ABSTRACT
Nucleotide excision repair (NER) is a major repair pathway that recognizes and corrects various lesions in cellular DNA. We hypothesize that damage recognition is an initial step in NER that senses conformational anomalies in the DNA caused by lesions. We prepared three DNA duplexes containing the carcinogen adduct N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene (FAAF) at G(1), G(2) or G(3) of NarI sequence (5'-CCG(1)G(2)CG(3)CC-3'). Our (19)F-NMR/ICD results showed that FAAF at G(1) and G(3) prefer syn S- and W-conformers, whereas anti B-conformer was predominant for G(2). We found that the repair of FAAF occurs in a conformation-specific manner, i.e. the highly S/W-conformeric G(3) and -G(1) duplexes incised more efficiently than the B-type G(2) duplex (G(3)∼G(1)> G(2)). The melting and thermodynamic data indicate that the S- and W-conformers produce greater DNA distortion and thermodynamic destabilization. The N-deacetylated N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (FAF) adducts in the same NarI sequence are repaired 2- to 3-fold less than FAAF: however, the incision efficiency was in order of G(2)∼G(1)> G(3), a reverse trend of the FAAF case. We have envisioned the so-called N-acetyl factor as it could raise conformational barriers of FAAF versus FAF. The present results provide valuable conformational insight into the sequence-dependent UvrABC incisions of the bulky aminofluorene DNA adducts.

Show MeSH
Related in: MedlinePlus