A quantitative test of Zimm's model for the rotor-speed-department sedimentation of linear DNA molecules.

Abstract

AbstractIn 1974, Zimm described a theory which predicts that the sedimentation coefficient of high‐molecular‐weight DNA will decrease as the rotor speed of measurement increases. In 1979, this theory was revised, and the new formula predicts speed‐dependence effects that are substantially smaller than the predictions of the original version. This report describes the results of subjecting both the original and the revised versions of the theory to quantitative tests using a well‐defined sucrose‐gradient system and a DNA of known molecular weight (T4c DNA). T4c bacteriophage is a mutant, whose DNA contains the unmodified base cytosine, instead of the glucosylated hydroxymethylcytosine characteristic of the T‐even bacteriophages, and has a molecular weight of 115 ± 3 × 106. The DNA of the wild‐type phage (T4D+) was also used in some experiments.In addition to the quantitative tests, the experiments test for an effect first observed by Rubenstein and Leighton, which showed that the sedimentation coefficient measured for T2 DNA depended on the composition of the centrifuge tube used for the measurement (tube composition effect). It can be inferred from this observation that an interaction occurs between particle and tube wall during sedimentation, and this leads to a reduction in sedimentation velocity independent of the reduction in S described by Zimm's theory.The results show that in the range of 25,000–50,000 rpm, the original but theoretically incorrect form of the theory quite accurately describes the sedimentation behavior of both T4c and T4D+ DNA, although T4D+ was a special case in some respects. The revised (corrected) form of the theory predicts much less of a speed‐dependence effect than that actually observed. The discrepancy between corrected theory and observation suggests that other factors (perhaps arising from the use of the swinging bucket rotor geometry) are causing the additional observed reduction in S20,w. However, the experiments show that the tube composition effect does not seem to be one of these.