title: Expanded Genetic Alphabets: Managing Nucleotides That Lack Tautomeric, Protonated, or Deprotonated Versions Complementary to Natural Nucleotides.
abstract: 2,4-Diaminopyrimidine (trivially K) and imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (trivially X) form a nucleobase pair with Watson-Crick geometry as part of an artificially expanded genetic information system (AEGIS). Neither K nor X can form a Watson-Crick pair with any natural nucleobase. Further, neither K nor X has an accessible tautomeric form or a protonated/deprotonated state that can form a Watson-Crick pair with any natural nucleobase. In vitro experiments show how DNA polymerase I from E. coli manages replication of DNA templates with one K:X pair, but fails with templates containing two adjacent K:X pairs. In analogous in vivo experiments, E. coli lacking dKTP/dXTP cannot rescue chloramphenicol resistance from a plasmid containing two adjacent K:X pairs. These studies identify bacteria able to serve as selection environments for engineering cells that replicate AEGIS pairs that lack forms that are Watson-Crick complementary to any natural nucleobase.
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States.
authors.forename: Christian B
authors.initials: CB
authors.lastname: Winiger
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States.|Firebird Biomolecular Sciences LLC , 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States.
authors.forename: Ryan W
authors.initials: RW
authors.lastname: Shaw
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States.|Firebird Biomolecular Sciences LLC , 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States.
authors.forename: Myong-Jung
authors.initials: MJ
authors.lastname: Kim
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States.|Firebird Biomolecular Sciences LLC , 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States.
authors.forename: Jennifer D
authors.initials: JD
authors.lastname: Moses
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States.|Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States.
authors.forename: Mariko F
authors.initials: MF
authors.lastname: Matsuura
authors.affiliation: Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Blvd. Box 17, Alachua, Florida 32615, United States.|Firebird Biomolecular Sciences LLC , 13709 Progress Blvd. Box 7, Alachua, Florida 32615, United States.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Benner
mesh_terms: D020029:Base Pairing / Q000235:genetics; D004247:DNA / Q000235:genetics; D004256:DNA Polymerase I / Q000378:metabolism; D004261:DNA Replication / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D009711:Nucleotides / Q000235:genetics*; D011743:Pyrimidines / Q000378:metabolism
chemical_list: D009711:Nucleotides; D011743:Pyrimidines; C017205:2,4-diaminopyrimidine; D004247:DNA; D004256:DNA Polymerase I
keywords: DNA; artificially expanded genetic information systems (AEGIS); in vivo conversion; polymerases; synthetic biology