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–Hg^II–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.