Cai Y, et al. (2013) Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: Energetic and structural relationships to nucleotide excision repair susceptibility. Chem Res Toxicol ()
Abstract: The crystal structure of Rad4/Rad23, the yeast homolog of the human nucleotide excision repair (NER) lesion recognition factor XPC-RAD23B (Min and Pavletich, (2007) Nature 449:570-575) reveals that the lesion-partner base is flipped out of the helix and binds the protein. This suggests the hypothesis that flipping of this partner base must overcome a free energy barrier, which constitutes one element contributing to changes in the thermodynamic properties induced by the DNA damage and sensed by the recognition protein. We explored this hypothesis by computing complete flipping free energy profiles for two lesions derived from the procarcinogenic polycyclic aromatic hydrocarbons (PAHs), dibenzo[a,l]pyrene (DB[a,l]P) and benzo[a]pyrene (B[a]P), R-trans-anti-DB[a,l]P-N6-dA (R-DB[a,l]P-dA) and R-trans-anti-B[a]P-N6-dA (R-B[a]P-dA), and the corresponding unmodified duplex. The DB[a,l]P and B[a]P adducts differ in number and organization of their aromatic rings. We integrate these results with prior profiles for the R-trans-anti-DB[a,l]P-dG adduct (Zheng et al., (2010) Chem. Res. Toxicol. 23:1868-1870). All adopt conformational themes involving intercalation of the PAH aromatic ring system into the DNA duplex; however, R-DB[a,l]P-dA and R-B[a]P-dA intercalate from the major groove, while R-DB[a,l]P-dG intercalates from the minor groove. These structural differences produce different computed van der Waals stacking interaction energies between the flipping partner base with the lesion aromatic ring system and adjacent bases; we find that the better the stacking, the higher the relative flipping free energy barrier and hence lower flipping probability. The relative NER susceptibilities correlate inversely with stacking interactions and ease of flipping in these three differently intercalated lesions. In addition to partner base-flipping, the Rad4/Rad23 crystal structure shows that a protein-beta-hairpin, BH3, intrudes from the major groove side between the DNA strands at the lesion site. We present a molecular modeling study for the R-DB[a,l]P-dG lesion in Rad4/Rad23 showing BH3 beta-hairpin intrusion with lesion eviction, and we hypothesize that lesion steric effects play a role in the recognition of intercalated adducts.
|Status: Epub ahead of print||Type: Journal Article||PubMed ID: 23758590|
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