BODIPY phototether enables oligonucleotide cyclization and subsequent deprotection by tissue-transparent red light.

meso-methyl-BODIPY photocages release a leaving group upon visible light irradiation but often lack thermal stability. In turn, our thermally-stable, red-shifted BODIPY phototether allows oligonucleotide cyclization, preventing complementary strand hybridization. Hybridization resumes upon red-NIR irradiation, disconnecting the phototether by oxidative cleavage, which is easily monitored by a blue shift in fluorescence.