DNA fragmentation in a steady shear flow

Abstract

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 [Formula: see text], corresponding to a Reynolds number of [Formula: see text] and a Weissenberg number of [Formula: see text], [Formula: see text]% of the sample is broken into a polydisperse mixture with a number-averaged molecular weight of [Formula: see text] kbp and a polydispersity index of [Formula: see text], 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.