DNA Agarose Gel Electrophoresis

( demonstration )

Principle is to separate DNA or proteins on

the basis of their charge and their ability to

migrate within a gel (jello-like) matrix.

(molecular weight and structure)

A strong electric field is applied to DNA or

the protein mixture for an extended period of

time (hours) until the DNA move apart or

migrate.

Electrophoresis

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Power How fast will the DNA migrate?

DNA

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• DNA is negatively charged.

• When placed in an electrical field, DNA will migrate toward the positive pole (anode).

1. strength of the electrical field2. buffer (PH …..)3. density of agarose gel…

4. Size of the DNA !

♣ Within an agarose gel, linear DNA migrate inversely proportional to the log10 of their molecular weight.

How fast will the DNA migrate?

♣ gel electrophoresis separates DNA according to size♣Small DNA move faster than large DNA

agarose :

Size of the DNA

1 )

The structure of plasmid DNA

Oc DNA(open circular DNA)

cccDNA (covalently closed circular DNA)

L DNA (linear DNA) Ccc DNA<L DNA <oc DNA

2 )

Apparatus of agarose gel electrophoresis:

An agarose gel is prepared by combining agarose powder and a buffer solution.

Agarose

Buffer

Flask for boiling

Step1: making the gel

1) Tris-boratic acid （ TBE ）2) Tris-acetic acid （ TAE ）3) Tris-phosphate （ TPE ）

Electrophrosis buffer solution

5×TBE: Tris 108gEDTA 9.3gBoratic acid 55gH2O to 1000ml

pH : 8.0 ～ 8.2Add H2O to 1×TBE if use

Agarose Buffer Solution

Combine the agarose powder and buffer solution. Use a flask that is several times larger than the volume of buffer.

Agarose is insoluble at room temperature (left).The agarose solution is boiled until clear (right).

Gently swirl the solution periodically when heating to allow all the grains of agarose to dissolve. ***Be careful when boiling - the agarose solution may become superheated and may boil violently if it has been heated too long in a microwave oven.

Melting the Agarose

Casting tray

Gel combs

Power supply

Gel tank Cover

Electrical leads

Electrophoresis Equipment

Seal the edges of the casting tray and put in the combs. Place the casting tray on a level surface.

Preparing the Casting Tray

Gel casting tray & combs

Allow the agarose solution to cool slightly (~60ºC) and then carefully pour the melted agarose solution into the casting tray. Avoid air bubbles.

Pouring the gel

Each of the gel combs should be submerged in the melted agarose solution.

When cooled, the agarose polymerizes, forming a flexible gel. It should appear lighter in color when completely cooled (30-45 minutes). Carefully remove the combs and tape.

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buffer

Add enough electrophoresis buffer to cover the gel to a depth of at least 1 mm. Make sure each well is filled with buffer.

Cathode(negative)

Anode(positive)

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DNA

Step 2: Setting up the Apparatus

The agarose gel is placed in an electrophoresis apparatus.

6X Loading Buffer: Glycerol (for weight) Bromophenol Blue (for color)

Sample Preparation

Mix the samples of DNA with the 6X sample loading buffer (w/ tracking dye). This allows the samples to be seen when loading onto the gel, and increases the density of the samples, causing them to sink into the gel wells.

0.5 μg 的 1kb DNA Ladder 0.8%TAE 琼脂糖凝胶， EB 染色

DNA marker

The function of DNA marker

Loading the Gel

Carefully place the pipette tip over a well and gently expel the sample. The sample should sink into the well. Be careful not to puncture the gel with the pipette tip.

Place the cover on the electrophoresis chamber, connecting the electrical leads. Connect the electrical leads to the power supply. Be sure the leads are attached correctly - DNA migrates toward the anode (red). When the power is turned on, bubbles should form on the electrodes in the electrophoresis chamber.

Running the Gel

wells Bromophenol Blue

Cathode(-)

Anode(+)

Gel

After the current is applied, make sure the Gel is running in the correct direction. Bromophenol blue will run in the same direction as the DNA.

DNA(-)

The most convenient method to visualize DNA in gel electrophoresis is staining with the fluorescent dye ethidium bromide.

STAIN FOR DNA

This compound contains a planar group that intercalates between the stacked bases of DNA.

Ethidium bromide

EB

• Ethidium bromide binds to DNA and fluoresces under UV light, allowing the visualization of DNA on a Gel.

• Ethidium bromide can be added to the gel and/or running buffer before the gel is run or the gel can be stained after it has run.

Staining the Gel

• Place the gel in the staining tray containing warm diluted stain.• Allow the gel to stain for 25-30 minutes.• To remove excess stain, allow the gel to destain in water.• Replace water several times for efficient destain.

Ethidium Bromide requires an ultraviolet light source to visualize

Because ethidium is a DNA intercalating agent, it is a powerful mutagen. Incorporation of ethidium in the DNA of living organisms (i.e. you and us) can cause (unwanted) mutations.

Attention:

Visualizing the DNA (QuikVIEW stain)

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1,500 1,000

500 750

2,000 bp

DNA ladder

PCRProduct

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March 12, 2006

Samples # 1, 6, 7, 10 & 12 were positive for Wolbachia DNA

Relaxed circleLinearized form

Super-coiled form