Given the essential role of apurinic/apyrimidinic
endonuclease (APE1) in gene repair and
cancer progression, we report a novel approach for probing and regulating cellular APE1 activity by using
DNA tetrahedrons. The tetrahedron with an AP site-containing antenna exhibits high sensitivity and specificity to APE1. It is suitable for APE1 in vitro detection (detection limit 5 pM) and cellular fluorescence imaging without any auxiliary transfection
reagents, which discriminates the APE1 expression level of
cancer cells and normal cells. In contrast, the tetrahedron with an AP site on its scaffold exhibits high binding affinity to APE1 but limits enzymatic catalysis making this nanostructure an APE1 inhibitor with an IC50 of 14.8 nM. It suppresses the APE1 activity in living cells and sensitizes
cancer cells to anticancer drugs. We also demonstrate that the APE1 probe and inhibitor can be switched allosterically via stand displacement, which holds potential for reversible inhibition of APE1. Our approach provides a new way for fabricating
enzyme probes and regulators and new insights into
enzyme-substrate interactions, and it can be expanded to regulate other
nucleic acid related
enzymes.