Julia Chivu ’23

Figure 1  DNA strand unwinding causing the formation of the replication fork followed by DNA replication.

Genomic DNA is constantly at risk of molecular decay. To address this issue, base excision DNA repair (BER) plays a critical role in fixing the minor DNA damage. In particular, Ape1 (or apurinic/apyrimidinic endonuclease) is a multifunctional protein that is a key component in BER. Ape1 has various impacts on gene expression, RNA processing, maintaining genetic stability, and more. Some scholars have created inhibitors to study Ape1’s functions. However, the off-target effects of these inhibitors have not been widely studied. PhD student Zhouyiyuan Xue and Dr. Bruce Demple of Stony Brook University investigated the AP endonuclease inhibitor Compound 3 and redox inhibitor APX2009. The researchers aimed to understand how these inhibitors interact with Ape1 and their effects on cells.

Two cell types were utilized in the experiment: wild-type and APEX1-KO, within mouse and human cell lines. The APEX1-KO cells lacked the Ape1 protein. All of the experimental cells were plated and incubated for 24 hours. They were then treated with a diluted form of a known DNA-damaging agent, methylmethane sulfonate (MMS), to identify its effects on the wild-type and APEX1-KO cells. An MTT assay was performed, as this technique acts as an indicator of cell viability. In addition, Western blotting was performed to detect and also quantify the specific proteins, in this case Ape1, found in a cell sample. 

Although western blotting demonstrated that the APEX1-KO cells did not contain the Ape1 protein, the cells remained viable. The APEX1-KO cells were predicted to die because they lacked the ability to repair DNA damage. This finding suggests that there may be other repair enzymes that are activated within the cells to compensate for the absence of Ape1. In addition, the APEX1-KO cells were not as damaged by the MMS as expected. Because Ape1 assists in cell damage repair, it was anticipated that the cells lacking this protein would be highly vulnerable to the MMS. This suggests that there may be additional repair mechanisms involved to aid in the repair of the DNA within these cells that have yet to be discovered. Also, the inhibitors unintentionally harmed cells, including those without the Ape1 protein. Ultimately, these findings provide valuable insights into Ape1 proteins and their inhibitors, which are not yet completely understood. These discoveries may also be promising for potential applications in cancer treatment, as they shed light on previously unknown DNA repair mechanisms. 

Works Cited: 

[1] Z. Xue, B. Demple, Roles of ape1 in base excision dna repair and modulation of gene expression. Antioxidants 11, (2022). doi:10.3390/antiox11091817.

[2] Image retrieved from:

https://unsplash.com/photos/a-double-strand-of-blue-and-white-spirals-pRt3JVYlJho