DNA synthesis: evaluation of a hydrodynamic method for measuring the rate of replication fork movement

When replicating DNA is labeled sequentially with radioactive and density tracers and analyzed by equilibrium centrifugation, the fraction banding at heavier than normal density is inversely proportional to the rate of replication fork movement if there is a sharp transition from one tracer to the other on the newly synthesized chains (Painter and Schaefer, '69). Primate CV-1 DNA labeled for 5 to 30 minutes with 3H-dThd and then for three hours with BrdUrd in the presence of FdUrd bands in a bimodal distribution in alkaline CsCl, rather than in a continuous distribution with a skew toward heavier density seen when FdUrd is omitted and centrifugation is in neutral CsCl. The heavy density peak represents interspersion of both tracers in the DNA and is caused by slow transition from dThd to BrdUrd incorporation when the tracers are switched in the labeling medium. This may result from preferential uptake and incorporation of dThd over BrdUrd. Because of the interspersion, calculation of the rate of replication fork movement is inaccurate. Reversal of the labeling sequence with administration of the long density pulse before the radioactive pulse reduces the problem of interspersion. Using this sequence of labeling, estimates of the rate of fork movement of 0.36-0.38 micrometer/min are obtained when the 3H pulse time is long enough to allow accurate measurement of the fraction of heavy DNA. Analysis by fiber autoradiography yields a rate of 0.56 micrometer/min in the same cell line. If appropriate precautions are taken to minimize mixing of the two tracers in the precursor pool and to ensure that the fraction of heavy DNA is measured accurately, the hydrodynamic technique provides an objective method of measuring rate of fork movement that gives values only slightly lower than those obtained by autoradiography.