Why might repair mechanisms following a CRISPR cut lead to non-functional viral DNA?

The correct answer highlights that repair mechanisms following a CRISPR cut frequently introduce errors during the DNA repair process. When CRISPR technology is used to create targeted double-strand breaks in DNA, the cell's natural repair pathways, such as non-homologous end joining (NHEJ) or homology-directed repair (HDR), take over to mend the breaks. While these pathways are essential for maintaining genomic integrity, they are not perfect and can result in insertions or deletions of nucleotides at the site of the break. This can lead to mutations that disrupt the reading frame of genes, resulting in non-functional or dysfunctional viral DNA.

These errors are a consequence of the nature of these repair processes, particularly NHEJ, which tends to be error-prone because it does not rely on a template for repair. Instead, it simply 'glues' the DNA ends back together, which can produce errors. Such mutations in viral DNA can hinder the virus's ability to replicate or produce essential proteins, thereby rendering it non-functional.