Past exam of the biochemistry course of the University of Cambridge / 2024 / Paper 5 / Section 1 / e / Solution

Latent viral DNA has regularly spaced nucleosome protection, whereas much of the nuclear viral DNA during productive infection lacks that regular protection. In the latent sample, increasing digestion resolves a ladder of protected fragments, as expected when micrococcal nuclease cuts exposed linker DNA between nucleosomes. In the productive sample, viral signal is lost rapidly into heterogeneous small material rather than accumulating as a comparable ladder. That is consistent with a large pool of newly replicated or otherwise differently packaged viral DNA being more accessible.

The total-DNA ladders show that host chromatin remains nucleosomal and that the assay can recover protected fragments in each cellular condition. The virus-specific Southern blot distinguishes viral DNA from this abundant host background, and the uninfected lane controls probe background. The conclusion concerns the dominant detectable viral population: productive cultures can contain both chromatinized templates in viral latency and accessible replication products. Absence of a ladder does not establish absence of every histone molecule, and differences in DNA recovery or nuclease accessibility should be considered before assigning a precise fraction of chromatinized genomes.