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.