DNA fragmentation in a steady shear flow

We have determined the susceptibility of T4 DNA (166 kilobase pairs, kbp) to fragmentation under steady shear in a cone-and-plate rheometer. After shearing for at least 30 min at a shear rate of $6000s−1$⁠, corresponding to a Reynolds number of $O(103)$ and a Weissenberg number of $O(103)$⁠, $97.9±1.3$% of the sample is broken into a polydisperse mixture with a number-averaged molecular weight of $62.6±3.2$ kbp and a polydispersity index of $1.29±0.03$⁠, as measured by pulsed-field gel electrophoresis (with a 95% confidence interval). The molecular weight distributions observed here from a shear flow are similar to those produced by a (dominantly extensional) sink flow of DNA and are qualitatively different than the midpoint scission observed in simple extensional flow. Given the inability of shear flow to produce a sharp coil–stretch transition, the data presented here support a model where polymers can be fragmented in flow without complete extension. These results further indicate that DNA fragmentation by shear is unlikely to be a significant issue in microfluidic devices, and anomalous molecular weight observations in experiments are due to DNA processing prior to observation in the device.