Structural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence.

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TitleStructural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence.
Publication TypeJournal Article
Year of Publication2013
AuthorsJain, V, Hilton, B, Lin, B, Jain, A, Mackerell, AD, Zou, Y, Cho, BP
JournalChem Res Toxicol
Volume26
Issue8
Pagination1251-62
Date Published2013 Aug 19
ISSN1520-5010
Keywords2-Acetylaminofluorene, Base Pairing, Base Sequence, Cluster Analysis, Deoxyribonucleases, Type II Site-Specific, DNA Adducts, DNA Repair, Endodeoxyribonucleases, Escherichia coli, Escherichia coli Proteins, Molecular Dynamics Simulation, Mutation, Oligodeoxyribonucleotides, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Thermodynamics
Abstract

Cluster DNA damage refers to two or more lesions in a single turn of the DNA helix. Such clustering may occur with bulky DNA lesions, which may be responsible for their sequence-dependent repair and mutational outcomes. Here we prepared three 16-mer cluster duplexes in which two fluoroacetylaminofluorene adducts (dG-FAAF) are separated by zero, one, and two nucleotides in the Escherichia coli NarI mutational hot spot (5'-CTCTCG1G2CG3CCATCAC-3'): 5'-CG1*G2*CG3CC-3', 5'-CG1G2*CG3*CC-3', and 5'-CG1*G2CG3*CC-3' (G* = dG-FAAF), respectively. We conducted spectroscopic, thermodynamic, and molecular dynamics studies of these di-FAAF duplexes, and the results were compared with those of the corresponding mono-FAAF adducts in the same NarI sequence [Jain, V., et al. (2012) Nucleic Acids Res. 40, 3939-3951]. Our nucleotide excision repair results showed the diadducts were more reparable than the corresponding monoadducts. Moreover, we observed dramatic flanking base sequence effects on their repair efficiency in the following order: NarI-G2G3 > NarI-G1G3 > NarI-G1G2. The nuclear magnetic resonance, circular dichroism, ultraviolet melting, and molecular dynamics simulation results revealed that in contrast to the monoadducts, diadducts produced a synergistic effect on duplex destabilization. In addition, dG-FAAF at G2G3 and G1G3 destacks the neighboring bases, with greater destabilization occurring with the former. Overall, the results indicate the importance of base stacking and related thermal and thermodynamic destabilization in the repair of bulky cluster arylamine DNA adducts.

DOI10.1021/tx400186v
Alternate JournalChem. Res. Toxicol.
PubMed ID23841451
PubMed Central IDPMC3917139
Grant ListR01 CA086927 / CA / NCI NIH HHS / United States
P20 RR016457 / RR / NCRR NIH HHS / United States
R56 CA086927 / CA / NCI NIH HHS / United States
CA098296 / CA / NCI NIH HHS / United States
R56 CA098296 / CA / NCI NIH HHS / United States
CA86927 / CA / NCI NIH HHS / United States
R01 GM051501 / GM / NIGMS NIH HHS / United States
R29 GM051501 / GM / NIGMS NIH HHS / United States
R01 CA098296 / CA / NCI NIH HHS / United States