Biphenyl-DNA

Abstract

We report on the pairing properties of oligodeoxynucleotides containing chemically functionalized biphenyl residues instead of natural nucleobases. The synthesis of the corresponding C-nucleosides with one or two nitro- or methoxy groups, resp. in the distal phenyl ring was accomplished via Suzuki coupling of a protected 4-bromophenyl-C-nucleoside with the correspondingly substituted phenylboronic acids or esters. The interstrand hydrophobic and/or stacking recognition properties of the aromatic units were probed by Tm-measurements on duplexes containing single or triple incorporations. We found a strong dependence of duplex stability from the nature of the substituents (donor vs. acceptor). The stability of duplexes with one biphenyl-pair increases in the order of donor–donor < acceptor–donor < acceptor–acceptor pairs. On the other hand in the triply modified duplexes stability increases in the order acceptor–acceptor < donor–acceptor < donor–donor pairs. It thus appears that interactions to the nearest neighbor natural base-pairs are preferred by acceptor modified biphenyls while the interactions between biphenyls are most stable with opposing donor modified biphenyls.