Host DNA repair and replication machinery (DDR)

The host DNA repair and replication machinery is a complex network of cellular proteins, including DNA polymerases, nucleases, and ligases, that are essential for the life cycle of certain DNA viruses and the efficacy of viral-based gene therapies (Kay M. Nat Rev Genet. 2011). In the context of adeno-associated virus (AAV) transduction, this machinery is responsible for the critical rate-limiting step of second-strand synthesis, where the single-stranded viral genome is converted into a double-stranded template (Fong S, et al. Nat Med. 2022). Subsequently, these factors facilitate the circularization and concatemerization of the viral DNA into stable episomes, which persist in the nucleus of post-mitotic cells to provide long-term transgene expression (Fong S, et al. Mol Ther Med Clin Dev. 2020). Key components of this machinery include the MRN complex, DNA-PKcs, and various DNA polymerases such as Pol delta and epsilon. Because the efficiency of this process directly impacts the therapeutic outcome of gene therapies, it is a major focus for optimization strategies, including the use of small molecule enhancers or the engineering of viral capsids to better recruit these host factors. Conversely, inhibiting specific components of this machinery is being explored as a strategy to prevent the formation of persistent viral reservoirs, such as the covalently closed circular DNA (cccDNA) of the hepatitis B virus (HBV).

Other names

Host DNA repair and replication machinery mediating second-strand synthesis and episome formationAAV second-strand synthesis machineryDNA damage response (DDR) machineryHost cell DNA repair factorsViral episome formation machineryrcDNA-to-cccDNA conversion machinery

The host DNA repair and replication machinery acts as the primary enzymatic system for converting single-stranded viral DNA into double-stranded forms and subsequently into stable episomes. AAV-based gene therapies serve as substrates for these host enzymes, while small molecule modulators like proteasome inhibitors or DNA-damaging agents can enhance the recruitment and activity of these factors to improve transgene expression. Conversely, inhibitors of specific repair enzymes (e.g., DNA-PK or PARP inhibitors) can block this process, which is being investigated as a way to prevent the formation of viral reservoirs like HBV cccDNA.