Specific G-quadruplex structure recognition of human telomeric RNA over DNA by a fluorescently activated hyperporphyrin.

Abstract

Human telomeric repeat-containing RNA (TERRA), which has recently been found to play as important a role in living cells as its DNA counterpart, solely adopts a parallel G-quadruplex (G4) topology. However, developing a highly selective fluorescent probe specific for the TERRA G4 is a great challenge, since difficulty arises in differentiating it from the DNA G4s that possess polymorphic structures including parallel, (3 + 1) hybrid, basket, and chair topologies. In this work, 5,10,15,20-tetrakis(3,5-dihydroxyphenyl)porphyrin (TOH(d)PP) was selected out of various porphyrins as the most efficient fluorescent probe in targeting TERRA. We found that only the TERRA binding is effective in activating the hyperporphyrin spectrum of TOH(d)PP, favoring red-shifted spectral bands and an enhanced fluorescence emission. Following the previous investigations on the TERRA G4 structure and our present experiments, we anticipate that TOH(d)PP most likely interacts with the 5' tetrads of two TERRA G4s via a 1 : 2 sandwich association. The ribose 2'-OH favors the loop adenine residue-extended tetrad G4 plane that is specific for TERRA, thus besides π-stacking with the G4 tetrads, TOH(d)PP should also interact with this substructure to trigger an efficient electron communication between the tetraphenyl substituents and the porphyrin macrocycle, as required by the hyperporphyrin effect. The hydrogen bonding interactions of the eight hydroxyl substituents in TOH(d)PP with the backbone phosphate oxygen atoms of TERRA most likely further contribute to the binding selectivity. Our work demonstrates the potential of TOH(d)PP as a selective TERRA G4 fluorescent probe and a promising TERRA-based sensor reporter.