The association of Merkel cell polyomavirus (MCPyV) and Merkel cell carcinoma (MCC) established in 2008 has opened doors for the study of virus-induced oncogenesis. Much of what is known about polyomaviruses (PyVs) stems from decades of studies on SV40. However, recent research has shown differences among PyVs that might help explain the uniqueness of MCPyV that makes it the only PyV discovered to date that is associated with a human cancer. Therefore, it is important to understand the biology of this virus and its oncogenic potential. My study focuses on two of the early proteins of MCPyV, namely the large tumor antigen (LT) and the small tumor antigen (sT). Both proteins are multi-functional, contributing to viral replication and the stimulation of cellular proliferation. MCPyV LT is the viral helicase that binds to the viral origin (Ori) to initiate unwinding and the replication of the double-stranded DNA genome. Like other PyVs, MCPyV requires numerous cellular proteins to replicate its genome. In my research, I show that, in the presence of the viral Ori, the binding of LT to the Ori forms replication factories in the nucleus. A number of cellular factors involved in the host DNA damage response (DDR) re-localize to the sites of MCPyV LT-mediated replication. Inhibition of the DNA damage response by either drug treatment or siRNA knockdown decreases MCPyV replication, suggesting that an intact host DDR pathway is essential for the optimal replication of MCPyV. Previous research has shown that MCPyV sT indirectly enhances viral replication by stabilizing LT. In my study, I discover that sT is a metalloprotein that coordinates two iron-sulfur clusters. Mutations in the highly conserved cysteines found in MCPyV sTs abolishes its ability to stimulate LT-mediated viral DNA replication, and that sT can enhance LT-mediated replication in a manner that is independent of LT stabilization. Moreover, I show that sT translocates to the nuclear replication factories formed in the presence of LT and Ori, suggesting a more direct role of sT in promoting viral DNA replication. Interestingly, upon treatment with the potent antiviral agent cidofovir, sT-mediated enhancement of MCPyV replication is robustly inhibited, while replication driven by LT alone was not affected much. This finding supports the use of cidofovir in controlling PyV infection and offers MCPyV sT as a potential drug target to dampen viral growth. In summary, my work elucidates various aspects of MCPyV replication, including the involvement of the host DDR machinery and the role of sT that could potentially be targeted by drug treatment. This study contributes to the understanding of the virology of MCPyV and opens avenues for further research.