Abstract
The synthesis and incorporation into oligonucleotides of C‐nucleosides containing the two aromatic, non‐hydrogen‐bonding nucleobase substitutes biphenyl (I) and bipyridyl (Y) are described. Their homo‐ and hetero‐recognition properties in different sequential arrangements were then investigated via UV‐melting curve analysis, gel mobility assays, CD‐ and NMR spectroscopy. An NMR analysis of a dodecamer duplex containing one biphenyl pair in the center, as well as CD data on duplexes with multiple insertions provide further evidence for the zipper‐like interstrand stacking motif that we proposed earlier based on molecular modeling. UV‐thermal melting experiments with duplexes containing one to up to seven I‐ or Y base pairs revealed a constant increase in T~m~ in the case of I and a constant decrease for Y. Mixed I/Y base pairs lead to stabilities in between the homoseries. Insertion of alternating I/abasic site‐ or Y/abasic site pairs strongly decreases the thermal stability of duplexes. Asymmetric distribution of I‐ or Y residues on either strand of the duplex were also investigated in this context. Duplexes with three natural base pairs at both ends and 50 % of I pairs in the center are still readily formed, while duplexes with blunt ended I pairs tend to aggregate unspecifically. Duplexes with one natural overhang at the end of a I–I base pair tract can both aggregate or form ordered duplexes, depending on the nature of the natural bases in the overhang.