Agarose vs Polyacrylamide Gels

Agarose Polyacrylamide
Horizontal or vertical? Horizontal Vertical
One molecule or lots of Lots of molecules held together by One large molecule
molecules? intermolecular forces
Why are they poured Because you can. It’s easier to Need glass plates for
horizontal or vertical? pour a horizontal gel than it is to structure- very thin gels that
pour a vertical gel. need support.
Air speeds up polymerization.
If the gel was poured open to
air, it would not solidify
evenly.
Separates large molecules Both, but better for large Both, but better for small
or small ones? molecules molecules
Lets you tell small No Yes
differences between sizes
of bands?
Can be reheated and Yes No
poured?
Powder is toxic? No Yes
Solid is toxic No No
Type of molecules run in Mostly DNA DNA or proteins
this type of gel
Big gaps or small gaps in Bigger gaps than with Smaller gaps
gel? polyacrylamide
Special uses of this gel? Sequencing gels, protein gels
Things to know when Make sure buffer covers wells Make sure buffer covers wells
running the gel when running. when running.
If the gel runs too hot, the agarose Check for leaks before
might melt. running.

Things to know when Gel easily breaks where wells are.
handling the gel
Advantages to using this Can re-pour the gel if you goof.
gel Can decide if you want lots of
narrow lanes or a few wide lanes.
Fewer ingredients to mix.
Disadvantages of using Can’t tell small differences
this gel between band sizes.
Bands are usually not as sharp as
with polyacrylamide.
Expense? Agarose is about $1 a gram-
considered expensive.
Gel easily rips.
Easy to stain.
Can dry down the gel to save a
copy.
Need to know concentration
needed before buying the gels.
Need to know number of
samples so that you can buy
enough lanes for samples.
If you are making them
yourself, they take a long time
to make and are challenging to
pour.
Gels usually bought pre-
poured. Cost $5-7 per gel.