BNB/NBN‐Phenalenyl‐2'‐deoxyuridines as a Fluorophore–Quencher Pair in DNA

Deoxyribonucleic acid (DNA) enables the precise arrangement and positioning of chromophores in order to study their interactions, leading, for example, to through‐space energy transfer processes. BNB‐ and NBN‐doped phenalenyls are electronically complementary fluorophores that are neutral BN/CC isosteres of the phenalenyl cation and anion, respectively. Herein, we present a pair of BNB‐ and NBN‐doped phenalenyl‐extended nucleosides, which we introduced into DNA via phosphoramidite chemistry. The two chromophores act as a donor–acceptor pair in a Förster resonance energy transfer (FRET) process, which results in the quenching of the BNB‐phenalenyl fluorescence due to the nonradiative decay of the charge transfer (CT) state of the NBN‐phenalenyl acceptor in an aqueous environment. The DNA duplex serves as a supramolecular scaffold to control the arrangement of the interacting BNB‐ and NBN‐doped chromophores. The performance of the fluorophore–quencher pair was evaluated in a toehold‐mediated strand displacement (TMSD) experiment, demonstrating its potential for DNA‐based applications.