1. Agarose Gel Electrophoresis

2. Purposes To understand the principle of Gel electrophoresis
To become familiar with the part of the electrophoresis setup

3. What is Electrophoresis?
Electrophoresis is a laboratory technique for separating molecules based on their charge.

4. Separation of a Mixture of Charged Molecules
Charged molecules are separated based on their electrical charge and size.
Charge Separation
Size Separation
Analyze
Identify
Purify
Mixture of Charged Molecules
Positive Molecules
Negative Molecules

5. How Separation Occurs 1- Electrical Charge:
Many molecules (amino acids, proteins, DNA, and RNA) have naturally occurring negative and positive charges on them.
The sum of these charges determines the overall charge.
Molecules with a negative charge (anions) will be attracted to the positively charged node (anode).
Molecules with a positive charge (cations) will be attracted to the negatively charged node (cathode).

6. Proteins Entering Porous Material
How Separation Occurs
2- Molecule Size:
The porous material is made of microscopic particles suspended in a gel.
The microscopic particles attach to one another forming tunnels that act as a sieve to separate the molecules.
Small molecules can move faster than large molecules.
Size to molecular ratio
Porous Material
Proteins Entering Porous Material
Smallest Move Fastest

7. Gel Electrophoresis
Gels can be made from substances such as agarose or polyacrylamide.
Agarose – a complex sugar chain from red seaweed.
It is commonly used in foods (ice cream, and jellies) and many biological mediums.
It has a large pore size good for separating large molecules quickly.
Polyacrylamide – chain of acrylamide molecules.
It is often used to make plastics and rubber.
It has a small pore size good for separating small molecules.
Red Sea Weed
Acrylic Acid

8. Agarose Gel 1% agarose 2% agarose
A porous material derived from red seaweed
Agarose is highly purified to remove impurities and charge
Acts as a sieve for separating molecules.
This solid matrix will allow the separation of fragments by size.
Concentration affects molecules migration
Low conc. = larger pores better resolution of larger DNA fragments
High conc. = smaller pores better resolution of smaller DNA fragments
1% agarose
2% agarose

9. Fragment Resolution
Gel Concentration – Is dependant upon the size of the DNA fragments to be separated.

10. + - Agarose at Room Temperature is a 3-Dimentional solid matrix.
The smaller the fragments the further the migration or movement through the matrix. + -
Power
small
large

11. Purposes for Agarose Gel Electrophoresis
Analysis of molecules size
Separation and extraction of molecules
Quantification of molecules

12. Procedure

13. Components of an Electrophoresis System
Power supply and chamber, a source of power supply
Buffer, a fluid mixture of water and ions
Agarose gel, a porous material that molecules migrates through
Gel casting materials
Ions: atoms that have a positive or negative charge because they have lost or gained electrons.
Electrophoresis: migration of ions at different speeds is a basic principal

14. - + Cathode Anode Buffer Power Supply Dyes
During electrophoresis, water is electrolyzed which generates protons (H+ ions)at the anode (positive) and hydroxyl ions (OH -1)at the cathode (negative). The cathode (negative) end of the electrophoresis chamber then becomes basic and the anode (positive) end becomes acidic.
The electrode at which electrons enter the gel box from the power supply (along the black wire) is called the cathode and is negative (-). The electrode at which electrons leave the box and re-enter the power supply (along the red wire) is called the anode and carries a positive charge (+). The flow of electrons sets up a potential energy difference between the electrodes. This is known as potential, and is measured in volts. It establishes an electric field through which the ions in the gel box fluid migrate. The migration of ions in the fluid creates electrical current which is measured in milliamperes (milliamps).
Anode +
Buffer
Power Supply
Dyes

15. Electrophoresis Equipments
Power supply
Cover
Gel tank
Electrical leads 
Casting tray
Gel combs

16. Electrophoresis Buffer
TAE (Tris -acetate-EDTA) and TBE (Tris-borate- EDTA) – pH buffer
Tris Acetic acid provide ions to support conductivity and maintain pH
EDTA, prevent brake down of molecules
Concentration affects DNA migration
Use of water will produce no migraton
High buffer conc. could melt the agarose gel
A buffer is a chemical system that maintains a relatively constant pH even when strong acids or bases are added. Buffer solutions contain either a weak acid or weak base and one of their salts. Because a change in pH can alter the charge on a particle, it is important to use a buffer solution when separating during electrophoresis.

17. Overview of Agarose Gel Electrophoresis
Gel Preparation
Loading the gel
Running the gel

18. Gel Preparation Agarose is a linear polymer extracted from seaweed.

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

20. Melting the Agarose 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.

21. Gel casting tray & combs

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

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

25. Place the gel in the electrophoresis chamber.

26. 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.

28. Running the Gel

29. Migration of molecules in Agarose
Rate of migration of a molecule is inversely proportional to the log of its molecular weight
Distance α 1 / log-MW

30. 3
Best Fit Line 2
Log- Molecular Weight 1
Distance (mm)