Genomic methods for measuring DNA replication dynamics

Limitations of methods for measuring the concentration of human genomic DNA and oligonucleotide samples.

We compared different methods (absorbance, fluorescent dye-binding, and digital PCR) for measuring the concentrations of human genomic DNA from cultured cells and absorbance measurements of a synthetic DNA oligonucleotide. NIST Standard Reference Material (SRM) 2082, a pathlength absorbance standard, was used to benchmark the absorbance measurements done with microvolume spectrophotometers and ...

Initiation of DNA Replication: The Genomic Context

Bacterial genomic reorganization upon DNA replication.

Reorganization upon DNA Replication Myllykallio et al. (1) narrowed the replication origin of the archaeon Pyrococcus abyssi down to an 80-kb region (bar on left axis of Fig. 1A), an observation consistent with our prediction (2) of the replication origin of a closely related species, Pyrococcus OT3 (triangle on upper axis of Fig. 1A). Here, we report that a comparison of the genomic sequences ...

Bacterial Genomic Reorganization upon DNA Replication

Reorganization upon DNA Replication Myllykallio et al. (1) narrowed the replication origin of the archaeon Pyrococcus abyssi down to an 80-kb region (bar on left axis of Fig. 1A), an observation consistent with our prediction (2) of the replication origin of a closely related species, Pyrococcus OT3 (triangle on upper axis of Fig. 1A). Here, we report that a comparison of the genomic sequences ...

Knotting dynamics during DNA replication.

The topology of plasmid DNA changes continuously as replication progresses. But the dynamics of the process remains to be fully understood. Knotted bubbles form when topo IV knots the daughter duplexes behind the fork in response to their degree of intertwining. Here, we show that knotted bubbles can form during unimpaired DNA replication, but they become more evident in partially replicated in...