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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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Dynamic 19F-NMR spectra of fully paired 16-mer NarI duplexes. FAAF modification at (a) G1, (b) G2 and (c) G3. *unknown conformers; #impurity.
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gkr1307-F5: Dynamic 19F-NMR spectra of fully paired 16-mer NarI duplexes. FAAF modification at (a) G1, (b) G2 and (c) G3. *unknown conformers; #impurity.

Mentions: Figure 5 shows the 19F-NMR spectra of the three FAAF–NarI duplexes as a function of temperature (5–60°C). Whereas the three 19F signals in each duplex were in slow exchange at 5°C, the two downfield B- and S-signals became exchange broadened, giving rise to coalescent signals at around 30, 40 and 25°C for G1, G2 and G3, respectively. In all cases, the merged signals coalesced with the upfield W-signal at around 60°C. All three NarI duplexes showed relatively strong off-diagonal contour peaks of the major signals in the exchange spectra (data not shown), confirming their chemical exchanges.Figure 5.


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)

Dynamic 19F-NMR spectra of fully paired 16-mer NarI duplexes. FAAF modification at (a) G1, (b) G2 and (c) G3. *unknown conformers; #impurity.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkr1307-F5: Dynamic 19F-NMR spectra of fully paired 16-mer NarI duplexes. FAAF modification at (a) G1, (b) G2 and (c) G3. *unknown conformers; #impurity.
Mentions: Figure 5 shows the 19F-NMR spectra of the three FAAF–NarI duplexes as a function of temperature (5–60°C). Whereas the three 19F signals in each duplex were in slow exchange at 5°C, the two downfield B- and S-signals became exchange broadened, giving rise to coalescent signals at around 30, 40 and 25°C for G1, G2 and G3, respectively. In all cases, the merged signals coalesced with the upfield W-signal at around 60°C. All three NarI duplexes showed relatively strong off-diagonal contour peaks of the major signals in the exchange spectra (data not shown), confirming their chemical exchanges.Figure 5.

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