Triggered Excited-State Intramolecular Proton Transfer Fluorescence for Selective Triplex DNA Recognition

The triplex DNA has received much interest due to its various applications in gene regulation, molecular switch, and sensor development. However, realizing a highly selective recognition using a fluorescence probe specific only for the triplex topology is still a great challenge. Herein, we found that relative to the structural analogues of natural robinetin, myricetin, quercetin, kaempferol, morin, rutin, baicalin, luteolin, naringenin, genistein, chrysin, galangin, isorhamnetin, and several synthetic flavonoids, fisetin (FIS) is the brightest emitter when targeting the triplex DNA in contrast to binding with ss-DNA, ds-DNA (with or without an abasic site), i-motif, and DNA/RNA G-quadruplexes. Only the triplex association triggers the FIS green fluorescence that is relaxed from the tautomer favorable for excited-state intramolecular proton transfer (ESIPT). FIS can stabilize the triplex structure and primarily interact with the two terminals of the triplex via a 2:1 binding mode. This work demonstrates the potential of FIS as a DNA structure-selective switch-on ESIPT probe when evolving the triplex-forming oligonucleotides and developing the novel triplex-based sensors and switches.