(r5) ProceduresPolyacrylamideGelElectrophoresis < Lab

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---+ Polyacrylamide Gel Electrophoresis

Our gel rigs and supplies are from [[http://www.cbsscientific.com/][CBS Scientific]].

The [[http://www.nationaldiagnostics.com/articles.php/tPath/1_3][National Diagnostics Website]] has very helpful background on RNA/DNA polyacrylamide gels.

---++ Pouring the Gel

For %BLUE%denaturing%ENDCOLOR% urea gels, we use the [[http://www.nationaldiagnostics.com/images/ec833_protocol.pdf][SequaGel system]]. Check out the link to determine how to mix up a gel of the proper percentage. 

For %GREEN%nondenaturing%ENDCOLOR% gels, use the [[http://www.nationaldiagnostics.com/product_info.php/products_id/37][AccuGel system]]. The concentrated stock solution is 40%. Dilute the stock to get the desired gel percentage in your final volume. Add 1/10th volume 10x TBE buffer, then ddH<sub>2</sub>O for the rest of the volume.

%TABLE{dataalign="center"}%
| *Spacer Width* | *Gel Height* | *Gel Width* | *Gel Vol* | *TEMED Vol* | *10% APS Vol* |
| 1 mm | 28 cm | 16.5 cm | 50 ml | 20 µl | 400 µl |
| 1 mm | 14.5 cm | 16.5 cm | 25 ml | 10 µl | 200 µl |

TEMED is N,N,N',N'-tetramethylethylenediamine. APS is ammonium persulfate. Together, they create the radicals to initiate polymerization of the gel. TEMED and 10% APS should be stored at 4°C. APS solutions should be freshly prepared for best results.

%RED%Acrylamide is a neurotoxin before it is polymerized.%ENDCOLOR% You are working with it in a liquid solution where spills may happen. Wear gloves, a lab coat, and safety glasses when working with polyacrylamide gels.

---++ Loading the Gel

For denaturing gels, use the 2&times; formamide sample loading buffer.

For nondenaturing gels, use

Be sure to wash urea out of the wells using a syringe before loading the gel.

%TABLE{dataalign="center"}%
| *Spacer Width*  | *Gel Width* | *Well Height* | *Well Width* | *# Wells in Comb* | *Max Sample Vol* | 
| 1 mm | 16.5 cm | 15 mm | 8 mm | 12 | 120 µl |
| 1 mm | 16.5 cm  | 15 mm | 4 mm | 20 | 60 µl |
| 1 mm | 16.5 cm | 15 mm| 2 mm | 30 | 30 µl |

For sharp bands, you should load to much less than the maximum well volume.

---++ Running the Gel

You will need a high voltage power supply to run the large vertical polyacrylamide gels. Generally denaturing gels are run at a constant electrical power (Watts). This maintains a certain heated gel temperature during the run. For the 16.5 cm x 28.5 cm gels, use 25 W. Using a higher voltage can cause excessive heating that will crack the glass plates.

---++ Reagents

All reagents should be prepared with RNAse, DNase free water.

---+++ 2x Formamide Loading Buffer

| 32 ml | Deionized formamide |
| 8 ml | 10x TBE Buffer |
| 16 mg | Bromophenol Blue |

Makes 40 ml. Use for %BLUE%denaturing%ENDCOLOR% gels.

Note: Many recipes for this do not add the TBE buffer. This is fine if you are loading straight from a reaction which has buffer in it, but may cause problems if your sample is in pure H<sub>2</sub>O (for example, after EtOH precipitation).

The final concentration of EDTA in this buffer at 1x is 10 mM.

---+++ 5x Glycerol Loading Buffer

| 20 ml | 10x TBE Buffer |
| 20 ml | Glycerol |
| 16 mg | Bromophenol Blue |

Makes 40 ml. Use for %GREEN%nondenaturing%ENDCOLOR% gels.

Note: Many recipes for this do not add the TBE buffer or substitute sucrose for glycerol.

---+++ 10x TBE Buffer

| 108 g | Tris base |
| 55 g | Boric acid |
| 40 ml | 0.5 M EDTA, pH 8.0 |

Add ddH<sub>2</sub>O to 1 L.

---+++ 0.5 M EDTA, pH 8.0

   1 Dissolve 186.1 g Na<sub>2</sub>EDTA in 700 ml ddH<sub>2</sub>O. 
   1 Adjust pH to 8.0 with 10 M NaOH.
   1 Add ddH<sub>2</sub>O to 1 L.
Topic revision: r5 - 2012-03-12 - JeffreyBarrick