Examination of the Long-range Effects of Aminofluorene-induced Conformational Heterogeneity and Its Relevance to the Mechanism of Translesional DNA Synthesis

• Published in: Journal of molecular biology Vol. 366; no. 5; pp. 1387 - 1400
• Main Authors: Meneni, Srinivasarao, Liang, Fengting, Cho, Bongsup P.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 09.03.2007
• Subjects: aminofluorene-DNA adducts; Bacillus; Base Pair Mismatch; Base Pairing; Circular Dichroism; conformational heterogeneity; DNA - chemistry; DNA - genetics; DNA Adducts - chemistry; DNA Damage - genetics; DNA Replication - genetics; Fluorenes - metabolism; Fluorenes - pharmacology; Hydrogen Bonding; long-range effect; Models, Molecular; Molecular Structure; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Temperature; Templates, Genetic; tranlesion synthesis; CD; conformational heterogeneity; BF; aminofluorene-DNA adducts; FAF; AAF-adduct; AF-adduct; tranlesion synthesis; ICD 290-360 nm; SMI; long-range effect; TLS; NOESY; H/D
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2006.12.023

Adduct-induced conformational heterogeneity complicates the understanding of how DNA adducts exert mutation. A case in point is the N-deacetylated AF lesion [ N-(2′-deoxyguanosin-8-yl)-2-aminofluorene], the major adduct derived from the strong liver carcinogen N-acetyl-2-aminofluorene. Three conformational families have been previously characterized and are dependent on the positioning of the aminofluorene rings: B is in the “ B-DNA” major groove, S is “stacked” into the helix with base-displacement, and W is “wedged” into the minor groove. Here, we conducted 19F NMR, CD, T m, and modeling experiments at various primer positions with respect to a template modified by a fluorine tagged AF-adduct (FAF). In the first set, the FAF-G was paired with C and in the second set it was paired with A. The FAF-G:C oligonucleotides were found to preferentially adopt the B or S-conformers while the FAF-G:A mismatch ones preferred the B and W-conformers. The conformational preferences of both series were dependent on temperature and complementary strand length; the largest differences in conformation were displayed at lower temperatures. The CD and T m results are in general agreement with the NMR data. Molecular modeling indicated that the aminofluorene moiety in the minor groove of the W-conformer would impose a steric clash with the tight-packing amino acid residues on the DNA binding area of the Bacillus fragment (BF), a replicative DNA polymerase. In the case of the B-type conformer, the carcinogenic moiety resides in the solvent-exposed major groove throughout the replication/translocation process. The present dynamic NMR results, combined with previous primer extension kinetic data by Miller & Grollman, support a model in which adduct-induced conformational heterogeneities at positions remote from the replication fork affect polymerase function through a long-range DNA–protein interaction.