AGAROSE GEL ELECTROPHORESIS

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Gel electrophoresis is a widely used technique for the analysis of nucleic acids and proteins.  Most every molecular biology research laboratory routinely uses agarose gel electrophoresis for the preparation and analysis of DNA.  We will be using agarose gel electrophoresis to determine the presence and size of PCR products.

Background:

Electrophoresis is a method of separating substances based on the rate of movement while under the influence of an electric field.  Agarose is a polysaccharide purified from seaweed.  An agarose gel is created by suspending dry agarose in a buffer solution, boiling until the solution becomes clear, and then pouring it into a casting tray and allowing it to cool.  The result is a flexible gelatin-like slab.  During electrophoresis, the gel is submersed in a chamber containing a buffer solution and a positive and negative electrode.  The DNA to be analyzed is forced through the pores of the gel by the electrical current.  Under an electrical field, DNA will move to the positive electrode (red) and away from the negative electrode (black).  Several factors influence how fast the DNA moves, including; the strength of the electrical field, the concentration of agarose in the gel and most importantly, the size of the DNA molecules.  Smaller DNA molecules move through the agarose faster than larger molecules.  DNA itself is not visible within an agarose gel.  The DNA will be visualized by the use of a dye that binds to DNA.

Purpose:  To determine the presence or absence of PCR products and quantify the size (length of the DNA molecule) of the product.

Materials needed:    Agarose

                                    TAE Buffer

                                    6X Sample Loading Buffer

                                    DNA ladder standard

                                    Electrophoresis chamber

                                    Power supply

                                    Gel casting tray and combs

                                    DNA stain

                                    Staining tray

                                    Gloves

                                    Pipette and tips

Recipes:                    TAE Buffer

                                    4.84 g Tris Base

                                    1.14 ml Glacial Acetic Acid

                                    2 ml 0.5M EDTA (pH 8.0)

                                     - bring the total volume up to 1L with water

Add Tris base to ~900 ml H₂O. Add acetic acid and EDTA to solution and mix. Pour mixture into 1 L graduated cylinder and add H₂O to a total volume of 1 L.

Note – for convenience a concentrated stock of TAE buffer (either 10X or 50X) is often made ahead of time and diluted with water to 1X concentration prior to use.

6X Sample Loading Buffer

                        1 ml sterile H₂O

                        1 ml Glycerol

enough bromophenol blue to make the buffer deep blue (~ 0.05 mg)

-for long term storage, keep sample loading buffer frozen.

QUIKView DNA Stain

25 ml WARDS QUIKView DNA Stain

475 ml warm water (50-55° C)

Agarose Gel Electrophoresis Protocol

Preparing the agarose gel

•  Measure 1.25 g Agarose powder and add it to a 500 ml flask

•  Add 125 ml TAE Buffer to the flask.  (the total gel volume well vary depending on the size of the casting tray)

•  Melt the agarose in a microwave or hot water bath until the solution becomes clear.  (if using a microwave, heat the solution for several short intervals - do not let the solution boil for long periods as it may boil out of the flask).

•  Let the solution cool to about 50-55°C, swirling the flask occasionally to cool evenly. 

•  Seal the ends of the casting tray with two layers of tape.

•  Place the combs in the gel casting tray.

•  Pour the melted agarose solution into the casting tray and let cool until it is solid (it should appear milky white).

•  Carefully pull out the combs and remove the tape. 

•  Place the gel in the electrophoresis chamber.

•  Add enough TAE Buffer so that there is about 2-3 mm of buffer over the gel.

Note – gels can be made several days prior to use and sealed in plastic wrap (without combs).  If the gel becomes excessively dry, allow it to rehydrate in the buffer within the gel box for a few minutes prior to loading samples.

Loading the gel

•  Add 6 ml of 6X Sample Loading Buffer to each 25 ml PCR reaction

•  Record the order each sample will be loaded on the gel, including who prepared the sample, the DNA template - what organism the DNA came from, controls and ladder.

•  Carefully pipette 20 ml of each sample/Sample Loading Buffer mixture into separate wells in the gel.

•  Pipette 10 ml of the DNA ladder standard into at least one well of each row on the gel.

Note – if you are running multiple gels, avoid later confusion by loading the DNA ladder in different lanes on each gel.

Running the gel

•  Place the lid on the gel box, connecting the electrodes. 

•  Connect the electrode wires to the power supply, making sure the positive (red) and negative (black) are correctly connected.  (Remember – “Run to Red”)

•  Turn on the power supply to about 100 volts.  Maximum allowed voltage will vary depending on the size of the electrophoresis chamber – it should not exceed 5 volts/ cm between electrodes! .

•  Check to make sure the current is running through the buffer by looking for bubbles forming on each electrode.

•  Check to make sure that the current is running in the correct direction by observing the movement of the blue loading dye – this will take a couple of minutes (it will run in the same direction as the DNA).

•  Let the power run until the blue dye approaches the end of the gel.

•  Turn off the power.

•  Disconnect the wires from the power supply.

•  Remove the lid of the electrophoresis chamber.

•  Using gloves, carefully remove the tray and gel.

Gel Staining

•  Using gloves, remove the gel from the casting tray and place into the staining dish.

•  Add warmed (50-55°) staining mix.

•  Allow gel to stain for at least 25-30 minutes (the entire gel will become dark blue).

•  Pour off the stain (the stain can be saved for future use).

•  Rinse the gel and staining tray with water to remove residual stain.

•  Fill the tray with warm tap water (50-55°).  Change the water several times as it turns blue.  Gradually the gel will become lighter, leaving only dark blue DNA bands.  Destain completely overnight for best results.

•  View the gel against a white light box or bright surface.

•  Record the data while the gel is fresh, very light bands may be difficult to see with time.

Note – Gels stained with blue stains are stable for long periods.  When destaining is complete, remove gel from water and allow the gel to dehydrate.  Dark bands can be seen for in a dried gel for weeks or months.