title: Toward a designed genetic system with biochemical function: polymerase synthesis of single and multiple size-expanded DNA base pairs.
abstract: The development of alternative architectures for genetic information-encoding systems offers the possibility of new biotechnological tools as well as basic insights into the function of the natural system. In order to examine the potential of benzo-expanded DNA (xDNA) to encode and transfer biochemical information, we carried out a study of the processing of single xDNA pairs by DNA Polymerase I Klenow fragment (Kf, an A-family sterically rigid enzyme) and by the Sulfolobus solfataricus polymerase Dpo4 (a flexible Y-family polymerase). Steady-state kinetics were measured and compared for enzymatic synthesis of the four correct xDNA pairs and twelve mismatched pairs, by incorporation of dNTPs opposite single xDNA bases. Results showed that, like Kf, Dpo4 in most cases selected the correctly paired partner for each xDNA base, but with efficiency lowered by the enlarged pair size. We also evaluated kinetics for extension by these polymerases beyond xDNA pairs and mismatches, and for exonuclease editing by the Klenow exo+ polymerase. Interestingly, the two enzymes were markedly different: Dpo4 extended pairs with relatively high efficiencies (within 18-200-fold of natural DNA), whereas Kf essentially failed at extension. The favorable extension by Dpo4 was tested further by stepwise synthesis of up to four successive xDNA pairs on an xDNA template.
authors.affiliation: Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
authors.forename: Haige
authors.initials: H
authors.lastname: Lu
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Krueger
authors.forename: Jianmin
authors.initials: J
authors.lastname: Gao
authors.forename: Haibo
authors.initials: H
authors.lastname: Liu
authors.forename: Eric T
authors.initials: ET
authors.lastname: Kool
mesh_terms: D019843:Archaeal Proteins / Q000378:metabolism; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000096:biosynthesis* / Q000737:chemistry*; D004256:DNA Polymerase I / Q000378:metabolism*; D019641:DNA, Archaeal / Q000378:metabolism; D004269:DNA, Bacterial / Q000378:metabolism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D013379:Substrate Specificity; D048229:Sulfolobus solfataricus / Q000378:metabolism
chemical_list: D019843:Archaeal Proteins; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004247:DNA; D004256:DNA Polymerase I
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