title: Pd(2+)-mediated base pairing in oligonucleotides.
abstract: Two short glycol nucleic acid (GNA) oligonucleotides, having either a terminal or an intrachain nucleobase replaced by the pyridine-2,6-dicarboxamide chelate of Pd(2+), have been synthesized and their hybridization properties studied by melting temperature measurements. In the termini of a double-stranded oligonucleotide, the Pd(2+) chelates provided dramatic stabilization of the duplex relative to its metal-free counterpart, in all likelihood owing to formation of Pd(2+)-mediated base pairs between pyridine-2,6-dicarboxamide and the opposing nucleobase. In contrast, no stabilization was observed when the Pd(2+) chelate was placed in the middle of the chain. Furthermore, the results could not be reproduced by adding a Pd(2+) salt in situ to the dilute oligonucleotide solutions but the palladated oligonucleotides had to be synthesized and purified prior to the hybridization studies. This behavior, presumably attributable to the relatively slow ligand-exchange reactions of Pd(2+), differs greatly from what is usually observed with more labile metal ions. The present results offer an explanation for the failure of previous attempts to incorporate Pd(2+)-mediated base pairs into oligonucleotides.
authors.affiliation: Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
authors.forename: Oleg
authors.initials: O
authors.lastname: Golubev
authors.affiliation: Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland; École nationale supérieure de chimie de Rennes, 11 allée de Beaulieu, 35708 Rennes France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Turc
authors.affiliation: Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland. Electronic address: tuanlo@utu.fi.
authors.forename: Tuomas
authors.initials: T
authors.lastname: Lönnberg
mesh_terms: D020029:Base Pairing; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D010165:Palladium / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D010165:Palladium
keywords: Base pairing; Hybridization; Oligonucleotide; Pd complexes