ctrophoresis
using Bio-Rad mini sub cell

Preparation of a 1% agarose gel

1.  Rinse and dry the gel casting tray (with 95% ethanol if available).

2.  Tape the ends of the casting tray as demonstrated. 
Set the casting tray on a level surface; you may want to put a paper
towel underneath in case it leaks.  NEVER pour the gel with the casting tray in the electrophoresis
chamber/box.

3.  Adjust the level of the comb so it rests evenly with a few
mm of space between teeth and the tray; this will allow wells to form
in the agarose.

4.  The 1% agarose has already been prepared (1 g agarose powder
per 100 mL 1x TBE), and melted; it is stored in 68^oC water
bath next door.  Gently swirl, make sure there are no particles. 
Using a 50 mL beaker, measure out 25 mL.  Return agarose stock
to water bath.

5.  Pour the 25mL agarose into the casting tray.

6.  Allow the gel to solidify (about 10 minutes); then remove
the comb and tape.

Loading and running the gel

1.  Add loading dye to each sample.

All loading dyes have a dense or viscous substance
(like 40% sucrose, or glycerol) that gives your DNA sample weight so
it sinks down into the well
Loading dyes also contain tracking dyes that visibly
migrate, allowing you to monitor progress.  In 1% a</span><span class="Normal--Char" style=" font-family: 'Arial', 'Arial';
font-size: 10pt;">garose, bromophenol blue (which looks purple) moves
like 300 bp dsDNA; xylene cyanol (which looks sky blue), migrates about
as fast as 4 kb (4000 base pairs) DNAs.

2.  Briefly centrifuge all samples to pool the contents.

3.  Insert the casting tray (with the gel on it) into the electrophoresis
chamber with the wells closest to the negative (black) electrode. 
DNA is negatively charged.  During electrophoresis, it will migrate
from the negative to the positive electrode.

4.  Gradually add 1xTBE (Tris-Borate-EDTA; electrophoresis buffer)
to the chamber until the buffer just covers the top of the gel.

5.  Load samples, taking care not to puncture the well bottoms. 
Do not attempt to load a sample if there is an air bubble in your pipet
tip.  Also, if a well has an air bubble in it, push it out using
a clean tip before loading a sample in it.

6.  Attach lid, make sure cords are correctly plugged into the
power supply (red to red, black to black)

7.  Plug in the power supply.

8.  Turn the power on and adjust the voltage control knob to
120 volts.  You should not need to touch any other knob.

9.  Electrophorese (run) until the bromophenol blue has migrated
to within ¾ of the positive electrode end of the gel.

10.  Shut off the power supply, unplug the leads, unplug the power supply.

11.  Lift the gel casting tray from the chamber.

Staining & photographing the gel (next door)

1.  Wear gloves & lab coat.

2.  Remove the gel from the casting tray and place it in a gently
shaking solution of ethidium bromide.  Use one of the small plastic
boxes (lids from tip boxes).  **Ethidium bromide is a mutagen.**

3.  Allow to stain for 5 minutes.

4.  Carefully decant the staining solution back into the ethidium
bromide stock bottle.

5.  Destain your gel (remove EtBr that is in the gel but not
bound to DNA) by soaking in distilled water.  Do this twice, 3-5
minutes each time.  Decant the water appropriately.

6.  EtBr-stained DNA bands will light up under UV illumination.  Never look observe EtBr fluorescence with unprotected eyes; short
wave UV is damaging.  We have a computerized system for
visualizing and photographing gels; you should not need to look at your
gel directly.  If you do, be sure to wear proper UV eye protection.

7.  When finished, dispose of your gel in the pile of EtBr-contaminated
gels (NOT in the trash).  Clean the surface of the UV lamp
with a paper towel.

8.  Never bring an ethidium bromide contaminated item back to
your work space.