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Related Concept Videos

DNA Agarose Gel Electrophoresis02:35

DNA Agarose Gel Electrophoresis

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Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify DNA fragments using a gel extraction protocol.
Gel extraction follows five major steps: running gel electrophoresis to separate fragments, isolating the individual bands, extracting DNA from those bands, and removing the dye and salts from the extracted mixture to obtain pure DNA.
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Two-dimensional gel electrophoresis is a high-resolution protein separation method first introduced by O' Farrell and Klose in 1975. This method involves protein separation by two dimensions, mass and charge, making it more accurate than one-dimensional gel electrophoresis.
The first dimension separation uses the isoelectric focusing or IEF technique performed on immobilized pH gradient (IPG) strips that separate proteins according to their isoelectric points.
Biological samples, such...
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Southern Blot02:57

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Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
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Gel electrophoresis is a method that separates biological macromolecules like nucleic acids or proteins by forcing them to pass through a gel matrix under an electric field.
A variation of gel electrophoresis, termed  polyacrylamide gel electrophoresis (PAGE), is commonly used for separating proteins according to their molecular size by passing them through a polyacrylamide gel. Because of the varying charges associated with amino acid side chains, PAGE can be used to separate intact...
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Preparation of DNA-crosslinked Polyacrylamide Hydrogels
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Ion-induced changes in DNA gels.

Ferenc Horkay1, Peter J Basser1, Erik Geissler2

  • 1Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 13 South Drive, Bethesda, MD 20892, USA. horkayf@mail.nih.gov.

Soft Matter
|July 10, 2023
PubMed
Summary
This summary is machine-generated.

Small angle neutron scattering reveals how DNA gel structure changes with ion concentration and pH. Increased calcium chloride or lower pH leads to DNA gel phase separation.

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Area of Science:

  • Biophysics
  • Materials Science
  • Polymer Science

Background:

  • DNA gels are complex networks with properties influenced by their ionic environment.
  • Understanding DNA gel behavior is crucial for applications in biotechnology and biomaterials.

Purpose of the Study:

  • To investigate the structural changes in DNA gels under varying ionic conditions using small angle neutron scattering (SANS).
  • To correlate changes in ion concentration and pH with DNA gel network properties and phase behavior.

Main Methods:

  • Small angle neutron scattering (SANS) measurements on DNA gels.
  • Variation of monovalent and divalent counter-ion concentrations and pH.
  • Anomalous small angle X-ray scattering (ASAXS) for ion cloud analysis.
  • Osmotic pressure measurements.

Main Results:

  • SANS data fitted with a two-term equation accounting for fluctuations and static inhomogeneities.
  • Low q-range SANS indicates large cluster formation.
  • Intermediate q-range scattering suggests rod-like structures with increasing CaCl2 concentration.
  • High q-region scattering reflects local chain geometry.
  • NaCl screening increases SANS intensity and mesh size; CaCl2 or decreased pH leads to phase separation.
  • SANS-derived I(0) agrees well with osmotic pressure measurements.
  • ASAXS shows weak influence of divalent ions on monovalent ion clouds, but tight following of polymer chains by divalent counter-ions.

Conclusions:

  • Ionic strength and pH significantly alter DNA gel structure, mesh size, and can induce phase separation.
  • SANS is a powerful tool for characterizing DNA gel networks and their response to environmental changes.
  • Counter-ion behavior is distinct for monovalent and divalent ions, impacting DNA gel properties.