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    DNA Gel Electrophoresis
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    DNA Gel Electrophoresis

    Thursday, 9/3/2020Introduction:Gel Electrophoresis (Credit: Khan Academy)Materials/Methods:Procedure: (adapted from Addgene)Insert Your Own Agarose Gel.jpg
    Thursday, 9/3/2020
    Introduction:
    Gel electrophoresis is a standard molecular biology technique that is used to separate biomolecules (DNA, RNA, and proteins) based on their size and charge. For DNA gel electrophoresis, it is often done “analytically” to assess relative sizes of samples in reference to a DNA standard or ladder. Electrophoresis uses an electrical field to move the negatively charged DNA through an agarose gel matrix toward a positive electrode. Shorter DNA fragments migrate through the gel more quickly than longer ones. Thus, you can determine the approximate length of a DNA fragment by running it on an agarose gel alongside a DNA ladder (a collection of DNA fragments of known lengths
    Gel Electrophoresis (Credit: Khan Academy)
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    For any DNA sequence such as a plasmid or PCR product, Benchling can recognize restriction sites for specific enzymes and simulate the expected fragments of DNA after digestion. These virtual digests are helpful in preparing students for what to look for in gel images and how to load lanes within a gel.
    Materials/Methods:
    Equipment
    ●
    Microwave
    ●
    Casting tray
    ●
    Well combs
    ●
    Power source
    ●
    Gel box
    ●
    UV lamp
    Reagents
    ●
    TAE (recipe here)
    ●
    Agarose
    ●
    Ethidum bromide (stock concentration of 10 mg/mL)
    Loading Samples and Running an Agarose Gel:
    1.
    Add loading buffer to each of your DNA samples.
    2.
    Once solidified, place the agarose gel into the gel box (electrophoresis unit).
    3.
    Fill gel box with 1xTAE (or TBE) until the gel is covered.
    4.
    Carefully load a molecular weight ladder into the first lane of the gel.
    5.
    Carefully load your samples into the additional wells of the gel.
    6.
    Run the gel at 80-150 V until the dye line is approximately 75-80% of the way down the gel. A typical run time is about 1-1.5 hours, depending on the gel concentration and voltage.
    7.
    Turn OFF power, disconnect the electrodes from the power source, and then carefully remove the gel from the gel box.
    8.
    Using any device that has UV light, visualize your DNA fragments. The fragments of DNA are usually referred to as ‘bands’ due to their appearance on the gel.
    Note: When using UV light, protect your skin by wearing safety goggles or a face shield, gloves and a lab coat.
    Analyzing Your Gel:
    Using the DNA ladder as a guide, you can infer the size of the DNA in your sample lanes. Upload an image of your own agarose gel run. Compare your acquired gel image to the simulated gel from the Virtual Digest to determine if it matches what was predicted.
    Insert Your Own Agarose Gel.jpg
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