Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism.
The Y-family DNA polymerase Dpo4, from the archaeon bacterium Sulfolobus solfataricus, is a member of the DinB family, which also contains human Pol kappa. It has a spacious active site that can accommodate two templating bases simultaneously, with one of them skipped by the incoming dNTP. Assays of single dNTP insertion opposite a benzo[ a]pyrene-derived N (2)-dG adduct, 10 S(+)- trans- anti-[BP]- N (2)-dG ([BP]G*), reveal that an incoming dATP is significantly preferred over the other three dNTPs in the TG 1*G 2 sequence context. Molecular modeling and dynamics simulations were carried out to interpret this experimental observation on a molecular level. Modeling studies suggest that the significant preference for dATP insertion observed experimentally can result from two possible dATP incorporation modes. The dATP can be inserted opposite the T on the 5' side of the adduct G 1*, using an unusual 5'-slippage pattern, in which the unadducted G 2, rather than G 1*, is skipped, to produce a -1 deletion. In addition, the dATP can be misincorporated opposite the adduct. The 5'-slippage pattern may be generally facilitated in cases where the base 3' to the lesion is the same as the adducted base.
Xu
Pingna
P
Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York City, New York 10003, USA.
Oum
Lida
L
Geacintov
Nicholas E
NE
Broyde
Suse
S
D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism; D020029:Base Pairing; D001483:Base Sequence; D001580:Benzopyrenes / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism; D003838:Deoxyadenine Nucleotides / Q000737:chemistry / Q000378:metabolism; D003849:Deoxyguanosine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D015394:Molecular Structure; D009711:Nucleotides / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity; D048229:Sulfolobus solfataricus / Q000201:enzymology / Q000378:metabolism
D019843:Archaeal Proteins; D001580:Benzopyrenes; D003838:Deoxyadenine Nucleotides; D009711:Nucleotides; C478198:benzo(a)pyrene N2-dG adduct; D004259:DNA-Directed DNA Polymerase; D003849:Deoxyguanosine; C026600:2'-deoxyadenosine triphosphate