Simultaneous in situ monitoring of base excision repair (BER) correlated enzymes like apurinic/apyrimidinic endonuclease 1 (APE1) and flap endonuclease 1 (FEN1) in living cells offers valuable insights into their roles in disease development and cytotoxicity caused by pollutants, but comprehensive analysis is currently hindered by diverse enzyme functions and limited methods. In this study, we developed a dual-activatable DNA fluorescent probe (AP-FLAP) to simultaneously visualize APE1 and FEN1 activities, revealing the BER-related DNA damage caused by various environmental pollutants within living cells. The AP-FLAP probe was designed by ingeniously integrating a dumbbell structure containing a 5′ flap and a hairpin structure containing AP sites into a single oligonucleotide probe. APE1 specifically hydrolyzed the AP sites, releasing a 5-carboxy-X-rhodamine (ROX) signal, while FEN1 recognized and cleaved the 5′ flap, releasing a 6-carboxyfluorescein (FAM) signal. The probe allowed for independent determination of APE1 and FEN1 activities with good specificity and sensitivity. Subsequently, we applied the AP-FLAP probe to investigate base damage induced by 1-methylphenanthrene (1-MP) and 6-chlorobenzo[a]pyrene (6-Cl-BaP) in human umbilical vein endothelial cells (HUVECs). Significant base damage by 1-MP and 6-Cl-BaP exposure was revealed, with a positive correlation of damage degree with different exposure concentrations from 0.1 to 100 μM. Notably, 6-Cl-BaP caused significant damage even at 0.1 μM, in a concentration-dependent manner. Our work provides a powerful tool for elucidating BER molecular mechanisms and DNA damage repair under environmental exposure and opens new avenues for developing multifunctional nucleic acid probes for a wide range of applications in chemical biology and biomedical research.
In vivo optical tumor molecular imaging encounters significant challenges in achieving adequate tumor specificity and sensitivity, largely attributed to off-tumor signal leakage and the relatively low expression levels of target molecules. Therefore, a double self-amplified programmable allosteric DNA nanomachine (named HPs-tFNA) is developed through two elaborately designed hairpin structures (HP1 and HP2) hybridized on tetrahedral framework DNA (tFNA), enabling rapid, specific, and sensitive tumor molecular imaging using the highly specific expression of apurinic/apyrimidinic endonuclease 1 (APE1) in the tumor cytoplasm as a stimulus-response target. In the presence of APE1, HP2 modifies two apurinic/apyrimidinic sites (AP sites), which can be specifically recognized and cleaved by APE1, releasing a significant number of cyclic sequences (cyclic-seq) and achieving initial APE1-assisted signal amplification. Subsequently, cyclic-seq hybridizes with HP1, inducing a conformational change that converts the stem-loop structure of HP1 to a linear form. This structural change facilitates the spatial separation of the fluorophore and quencher, thereby generating fluorescence signals. Furthermore, APE1 incises two AP sites within the HP1 loop region, resulting in the release of cyclic-seq. The released cyclic-seq can hybridize with additional HP1 to continuously amplify the fluorescence signal in a cyclic manner, thereby achieving the second round of signal amplification assisted by APE1. The experimental results of this study demonstrated that HPs-tFNA can achieve rapid in situ tumor molecular imaging and guide precise surgical excision in vivo, with superior spatial specificity. In particular, HPs-tFNA can effectively monitor drug resistance in neuroblastoma cells and stratify risk levels of neuroblastoma via plasma analysis.
危险品化学品经营许可证（带存储）