Assessment of DNA fibers to track replication dynamics

• Published in: Methods in cell biology Vol. 182; pp. 285 - 298
• Main Authors: Bennett, L G, Staples, C J
• Format: Journal Article
• Language: English
• Published: United States 2024
• Subjects: DNA replication; Genome stability; DNA damage; Replication stress; Cell biology; DNA fiber analysis; DNA repair
• ISSN: 0091-679X
• DOI: 10.1016/bs.mcb.2023.02.007

DNA replication is a complex and tightly regulated process that must proceed accurately and completely if the cell is to faithfully transmit genetic material to its progeny. Organisms have thus evolved complex mechanisms to deal with the myriad exogenous and endogenous sources of replication impediments to which the cell is subject. These mechanisms are of particular relevance to cancer biology, given that such "replication stress" frequently foreshadows genome instability during cancer pathogenesis, and that many traditional chemotherapies and a number of precision medicines function by interfering with the progress of DNA replication. Visualization of the progress and dynamics of DNA replication in living cells was historically a major challenge, neatly surmounted by the development of DNA fiber assays that utilize the fluorescent detection of halogenated nucleotides to track replication forks at single-molecule resolution. This methodology has been widely applied to study the dynamics of unperturbed DNA replication, as well as the cellular responses to various replication stress scenarios. In recent years, subtle modifications to DNA fiber assays have facilitated assessment of the stability of nascent DNA at stalled replication forks, as well as the detection of single-stranded DNA gaps and their subsequent filling by error-prone polymerases. Here, we present and discuss several iterations of the fiber assay and suggest methodologies for the analysis of the data obtained.