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Nucleic Acid Gel Electrophoresis

DNA electrophoresis using an agarose gel

Nucleic acid gel electrophoresis is a molecular biology technique for the separation, identification, and purification of DNA and RNA fragments based on size and charge. In this technique, DNA and RNA molecules are separated by applying an electric field to move negatively charged nucleic acids through an agarose or polyacrylamide gel matrix.  

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The gel matrix acts as a sieve, allowing shorter molecules to run more quickly through the pores of the gel than longer molecules. 

  • Agarose gels are more commonly used for DNA and RNA electrophoresis and can resolve DNA fragments ranging from 50 base pairs (50 bp) to 50,000 bp using standard electrophoretic techniques.
  • Polyacrylamide gels have a smaller range of separation and can resolve fragments of DNA less than ~500 bp with very high resolution.
  • Both agarose and polyacrylamide gels can also be used in electrophoretic mobility shift assays (EMSA) to characterize protein-nucleic acid interactions. 

Following electrophoresis, DNA and RNA molecules can be visualized via the use of stains or UV light, extracted and purified from the gel, or transferred for blotting. These methods are common preparative techniques in cloning, PCR, mass spectrometry, next generation sequencing (NGS), and Northern and Southern blot applications and workflows.

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