Polyacrylamide gel electrophoresis

This procedure is useful for the separation of small pieces of DNA, small quantities of DNA, or applications where higher resolution than can be achieved with agarose gel electrophoresis is needed. Because it is very difficult to remove DNA from polyacrylamide gel, it is advised that this protocol should only be used for diagnostic purposes and not for size separation of useful fragments.

Materials

Reagents

• 29:1 Acrylamide Solution
• 10X TBE buffer
• Ammonium Persulfate
• TEMED
• DNA solution
• SYBR green
• Bromophenol Blue

Equipment

• Vertical electrophoresis chamber
• Glass plates w/ spacers (which fit the chamber)
• Casting holder
• Pipettors

Procedure

1. Place Glass plates in casting apparatus
2. Add together the following to make 5ml of gel (0.75mm spacers)

• 500µl 10X TBE solution
  
• 35µl Ammonium Persulfate (10%w/v)
  
• X mL 29:1 acrylamide solution (See the table under "notes" to determine the desired acrylamide concentration)
  
• Y mL water (To make 5 mL)
  
• 2µl TEMED
  

3. Pipet the acrylamide solution between the casting plates using a 5ml pipetor
4. Insert comb into the top of the gel and allow it to cure vertically for approximately 30 minutes
5. Combine the following for all DNA samples including the ladder

• 10μL DNA solution
  
• 1μL SYBR green (100X Dilution in DMSO)
  
• 1μL Bromophenol Blue
  

6. Insert the gel into the electrophoresis chamber allong with the buffer dam

• Make sure both the gel and the buffer dam seal
• The wells on the gel should face the inside

7. add the necessary amounts of 1X TBE
8. Add DNA mix to wells.
9. Apply 80 volts and run for approximately 60 minutes

Troubleshooting

Referenced from the main protocol, an explanation of what can cause things to go wrong with the protocol.

Notes

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Specific Protocols

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