title: MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2'-deoxyuridine 5-substituents.
abstract: The stability of the mercury ion mediated dU-HgII-dU pair depends on substituents introduced at the 5-position of the pyrimidine moiety. To this end, a series of oligonucleotides were synthesized with dU modification in central position. Common and new phosphoramidites were utilized. Hybridization experiments provided 12-mer duplexes with non-canonical "dU-dU" pairs. In most cases Hg2+stabilizes duplexes by metal ion mediated base pair formation identified by higher duplex melting. Among the three types of dU derivatives incorporated in duplex DNA those with small aliphatic side chains have only a minor impact on the stability of the mercury-mediated base pair, while those with a triple bond in the side chain show hysteresis during duplex heating and cooling cycle implying triple bond interaction with mercury ions. Formation of metal ion mediated base pairs is blocked by space occupying aromatic side chains by side chain-helix stacking interactions. These interactions are too strong to permit mercury ion mediated base pair formation and drive the uridine N(3) acceptor atoms in an unfavorable pairing position.
authors.affiliation: Precision Medicine Research Laboratory, West China Hospital, West China School of Medicine, Sichuan University, 610041 Chengdu, People's Republic of China and Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
authors.forename: Xiurong
authors.initials: X
authors.lastname: Guo
authors.affiliation: Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany and Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany. Frank.Seela@uni-osnabrueck.de.
authors.forename: Sachin A
authors.initials: SA
authors.lastname: Ingale
authors.affiliation: Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany and Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany. Frank.Seela@uni-osnabrueck.de.
authors.forename: Haozhe
authors.initials: H
authors.lastname: Yang
authors.affiliation: Precision Medicine Research Laboratory, West China Hospital, West China School of Medicine, Sichuan University, 610041 Chengdu, People's Republic of China.
authors.forename: Yang
authors.initials: Y
authors.lastname: He
authors.affiliation: Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany and Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany. Frank.Seela@uni-osnabrueck.de.
authors.forename: Frank
authors.identifier: http://orcid.org/0000-0002-4810-4840
authors.initials: F
authors.lastname: Seela
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D003857:Deoxyuridine / Q000031:analogs & derivatives / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D008628:Mercury / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000737:chemistry; D013696:Temperature
chemical_list: D007477:Ions; D009943:Organophosphorus Compounds; C434331:phosphoramidite; D004247:DNA; D008628:Mercury; D003857:Deoxyuridine