title: Differential discrimination of DNA polymerase for variants of the non-standard nucleobase pair between xanthosine and 2,4-diaminopyrimidine, two components of an expanded genetic alphabet.
abstract: Mammalian DNA polymerases alpha and epsilon, the Klenow fragment of Escherichia coli DNA polymerase I and HIV-1 reverse transcriptase (RT) were examined for their ability to incorporate components of an expanded genetic alphabet in different forms. Experiments were performed with templates containing 2'-deoxyxanthosine (dX) or 2'-deoxy-7-deazaxanthosine (c7dX), both able to adopt a hydrogen bonding acceptor-donor-acceptor pattern on a purine nucleus (puADA). Thus these heterocycles are able to form a non-standard nucleobase pair with 2,4-diaminopyrimidine (pyDAD) that fits the Watson-Crick geometry, but is joined by a non-standard hydrogen bonding pattern. HIV-1 RT incorporated d(pyDAD)TP opposite dX with a high efficiency that was largely independent of pH. Specific incorporation opposite c7dX was significantly lower and also independent of pH. Mammalian DNA polymerases alpha and epsilon from calf thymus and the Klenow fragment from E. coli DNA polymerase I failed to incorporate d(pyDAD)TP opposite c7dX.
authors.affiliation: Department of Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.
authors.forename: M J
authors.initials: MJ
authors.lastname: Lutz
authors.forename: H A
authors.initials: HA
authors.lastname: Held
authors.forename: M
authors.initials: M
authors.lastname: Hottiger
authors.forename: U
authors.initials: U
authors.lastname: Hübscher
authors.forename: S A
authors.initials: SA
authors.lastname: Benner
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011743:Pyrimidines / Q000378:metabolism*; D012263:Ribonucleosides / Q000378:metabolism*; D013379:Substrate Specificity; D013698:Templates, Genetic; D014970:Xanthines
chemical_list: D009838:Oligodeoxyribonucleotides; D011743:Pyrimidines; D012263:Ribonucleosides; D014970:Xanthines; C017205:2,4-diaminopyrimidine; C005893:xanthosine; D004259:DNA-Directed DNA Polymerase