Fluorescent hydrophobic zippers inside duplex DNA: interstrand stacking of perylene-3,4:9,10-tetracarboxylic acid bisimides as artificial DNA base dyes.

Perylene-3,4:9,10-tetracarboxylic acid bisimides (PBs) were incorporated synthetically into oligonucleotides by using automated DNA building-block chemistry. The 2'-deoxyribofuranoside of the natural nucleosides was replaced by (S)-aminopropan-2,3-diol as an acyclic linker between the phosphodiester bridges that is tethered to one of the imide nitrogen atoms of the PB dye. The S configuration of this linker was chosen to mimic the stereochemical situation at the 3'-position of the natural 2'-deoxyribofuranosides. By using this strategy, up to six PB dyes were incorporated in the middle of 18-mer DNA duplexes by using interstrand alternating sequences of PBs with thymines or an abasic site analogue. Both PB dimers and PB hexamers as artificial base substitutions inside the duplexes yield characteristic excimer-type fluorescence. The stacking properties of the PB chromophores are modulated by the presence or absence of thymines opposite the PB modification site in the counterstrand. The interstrand PB dimers can be regarded as hydrophobically interacting base pairs, which display a characteristic fluorescence readout signal. Hence, for the PB hexamers, we proposed a zipperlike recognition motif that is formed inside duplex DNA. The PB zipper shows characteristic excimer-type emission as a fluorescence readout signal for the pairing interaction.