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Mass Spectrometry: Molecular Fragmentation Overview01:20

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The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can...
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DNA fragmentation in a steady shear flow.

Yiming Qiao1, Zixue Ma1, Clive Onyango1

  • 1Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA.

Biomicrofluidics
|October 31, 2022
PubMed
Summary
This summary is machine-generated.

T4 DNA fragmentation occurs under steady shear flow, producing a mixture of smaller DNA fragments. This process, observed in a rheometer, suggests DNA can break without full extension, impacting microfluidic device interpretations.

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Area of Science:

  • Biophysics
  • Polymer Physics
  • Molecular Biology

Background:

  • Understanding DNA fragmentation is crucial for molecular biology and biophysics.
  • Shear flow is a common physical process encountered in various experimental setups, including microfluidics.
  • Previous studies have explored DNA fragmentation under extensional flow, but shear flow dynamics remain less understood.

Purpose of the Study:

  • To investigate the susceptibility of T4 DNA to fragmentation under steady shear flow.
  • To characterize the molecular weight distribution of DNA fragments produced by shear.
  • To elucidate the mechanism of DNA fragmentation in shear flow and compare it to extensional flow.

Main Methods:

  • Utilized a cone-and-plate rheometer to apply steady shear to T4 DNA (166 kbp).
  • Sheared DNA samples for at least 30 minutes at specified shear rates.
  • Analyzed DNA fragmentation and molecular weight distribution using pulsed-field gel electrophoresis.

Main Results:

  • Steady shear flow fragmented T4 DNA into a polydisperse mixture.
  • The number-averaged molecular weight of fragments was significantly reduced.
  • Observed molecular weight distributions were similar to sink flow but different from simple extensional flow.

Conclusions:

  • DNA fragmentation in shear flow occurs without complete polymer extension, supporting a new fragmentation model.
  • Shear-induced DNA fragmentation is unlikely to be a major concern in microfluidic devices.
  • Anomalous molecular weight observations in experiments may stem from pre-experimental DNA processing rather than device effects.