title: An Isosteric and Fluorescent DNA Base Pair Consisting of 4-aminophthalimide and 2,4-diaminopyrimidine as C-Nucleosides.
abstract: A 13mer DNA duplex containing the artificial 4-aminophthalimide:2,4-diaminopyrimidine (4AP:DAP) base pair in the central position was characterized by optical and NMR spectroscopy. The fluorescence of 4AP in the duplex has a large Stokes shift of Δλ=124 nm and a quantum yield of ΦF=24 %. The NMR structure shows that two interstrand hydrogen bonds are formed and confirms the artificial base pairing. In contrast, the 4-N,N-dimethylaminophthalimide moiety prefers the syn conformation in DNA. The fluorescence intensity of this chromophore in DNA is very low and the NMR structure shows no significant interaction with DAP. Primer-extension experiments with DNA polymerases showed that not only is the 4AP C nucleotide incorporated at the desired position opposite DAP in the template, but also that the polymerase is able to progress past this position to give the full-length product. The observed selectivity supports the NMR results.
authors.affiliation: Institut für Organische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Merkel
authors.affiliation: Humboldt Universität zu Berlin, Department Chemie, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Dehmel
authors.affiliation: Humboldt Universität zu Berlin, Department Chemie, Brook-Taylor-Str. 2, 12489, Berlin, Germany.
authors.forename: Nikolaus P
authors.initials: NP
authors.lastname: Ernsting
authors.affiliation: Institut für Organische Chemie, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.
authors.forename: Hans-Achim
authors.initials: HA
authors.lastname: Wagenknecht
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D005453:Fluorescence; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000737:chemistry*; D010797:Phthalimides / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*
chemical_list: C529630:4-aminophthalimide; D009705:Nucleosides; D010797:Phthalimides; D011743:Pyrimidines; C017205:2,4-diaminopyrimidine; D004247:DNA
keywords: DNA; DNA polymerase; NMR spectroscopy; fluoroescence; oligonucleotide