DNA fragmentation in a steady shear flow

Yiming Qiao, Zixue Ma, Clive Onyango, Xiang Cheng, Kevin D. Dorfman

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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 6000 s-1, corresponding to a Reynolds number of O (10 3) and a Weissenberg number of O (10 3), 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.

Original languageEnglish (US)
Article number054109
Issue number5
StatePublished - Sep 1 2022

Bibliographical note

Funding Information:
This work was supported by NIH R21-HG011251. Parts of this work were performed in the Polymer Characterization Facility, University of Minnesota, a member of the NSF-funded Materials Research Facilities Network (www.mrfn.org) via the MRSEC program under NSF DMR-2011401.

Publisher Copyright:
© 2022 Author(s).

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  • Journal Article


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