title: Solution structure of a DNA duplex containing a replicable difluorotoluene-adenine pair.
abstract: A nonpolar aromatic nucleoside derivative based on 2,4-difluorotoluene (F), a non-hydrogen bonding shape analog of thymidine, was recently shown to be replicated against adenine with high efficiency and fidelity. This led to the suggestion that geometric matching, potentially even in the absence of hydrogen bonding between bases in a pair, may be sufficient to direct nucleotide selection during replication. We have examined the solution structure of the F-A pair in the context of a 12 base pair DNA duplex. We find that, despite the destabilization caused by this analog, the F-A pair very closely resembles that of a T x A pair in the same context. This lends support to the importance of shape matching in replication.
authors.affiliation: Department of Chemistry, University of Rochester, New York 14627, USA.
authors.forename: K M
authors.initials: KM
authors.lastname: Guckian
authors.forename: T R
authors.initials: TR
authors.lastname: Krugh
authors.forename: E T
authors.initials: ET
authors.lastname: Kool
mesh_terms: D000225:Adenine / Q000737:chemistry; D020029:Base Pairing; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004261:DNA Replication / Q000502:physiology*; D006860:Hydrogen Bonding; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis; D013936:Thymidine / Q000031:analogs & derivatives* / Q000737:chemistry; D014050:Toluene / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: D009838:Oligodeoxyribonucleotides; D014050:Toluene; C110527:difluorotoluene; D004247:DNA; D000225:Adenine; D013936:Thymidine