title: Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence.
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.
authors.affiliation: Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA.
authors.forename: Vipin
authors.initials: V
authors.lastname: Jain
authors.forename: Benjamin
authors.initials: B
authors.lastname: Hilton
authors.forename: Satyakam
authors.initials: S
authors.lastname: Patnaik
authors.forename: Yue
authors.initials: Y
authors.lastname: Zou
authors.forename: M Paul
authors.initials: MP
authors.lastname: Chiarelli
authors.forename: Bongsup P
authors.initials: BP
authors.lastname: Cho
mesh_terms: D015073:2-Acetylaminofluorene / Q000737:chemistry*; D000251:Adenosine Triphosphatases / Q000378:metabolism; D001483:Base Sequence; D002151:Calorimetry; D002942:Circular Dichroism; D018736:DNA Adducts / Q000737:chemistry*; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000378:metabolism; D003849:Deoxyguanosine / Q000737:chemistry*; D015252:Deoxyribonucleases, Type II Site-Specific; D029968:Escherichia coli Proteins / Q000378:metabolism; D005449:Fluorenes / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D021241:Spectrometry, Mass, Electrospray Ionization; D013816:Thermodynamics
chemical_list: D018736:DNA Adducts; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D005449:Fluorenes; C012177:2-aminofluorene; D015073:2-Acetylaminofluorene; D015252:Deoxyribonucleases, Type II Site-Specific; C046719:GGCGCC-specific type II deoxyribonucleases; C068631:UvrA protein, E coli; D000251:Adenosine Triphosphatases; D003849:Deoxyguanosine