Oligonucleotides containing a phenanthrene-derived, non-nucleosidic building block with flexible linkers were synthesized. The effect of the phenanthrene moiety on duplex stability at different positions was investigated. Placement of two phenanthrene residues in opposite positions had a slightly positive effect on duplex stability. This positive effect was further increased, when two phenanthrene pairs were juxtaposed. In contrast, introduction of a single phenanthrene unit opposite to an adenosine or a thymidine led to a destabilization of the duplex. A model of a phenanthrene-modified duplex is proposed.
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Langenegger et al. (2002) studied this question.