Agarose vs Polyacrylamide Gels
Agarose
Horizontal or vertical?
One molecule or lots of
molecules?
Why are they poured
horizontal or vertical?
Separates large molecules
or small ones?
Lets you tell small
differences between sizes
of bands?
Can be reheated and
poured?
Powder is toxic?
Solid is toxic
Type of molecules run in
this type of gel
Big gaps or small gaps in
gel?
Special uses of this gel?
Things to know when
running the gel
Things to know when
handling the gel
Advantages to using this
gel
Disadvantages of using
this gel
Expense?
Polyacrylamide
Horizontal
Vertical
Lots of molecules held together by One large molecule
intermolecular forces
Because you can. It’s easier to
Need glass plates for
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.
Both, but better for large
Both, but better for small
molecules
molecules
No
Yes
Yes
No
No
No
Mostly DNA
Yes
No
DNA or proteins
Bigger gaps than with
polyacrylamide
Smaller gaps
Make sure buffer covers wells
when running.
If the gel runs too hot, the agarose
might melt.
Sequencing gels, protein gels
Make sure buffer covers wells
when running.
Check for leaks before
running.
Gel easily breaks where wells are.
Gel easily rips.
Can re-pour the gel if you goof.
Can decide if you want lots of
narrow lanes or a few wide lanes.
Fewer ingredients to mix.
Can’t tell small differences
between band sizes.
Bands are usually not as sharp as
with polyacrylamide.
Easy to stain.
Can dry down the gel to save a
copy.
Agarose is about $1 a gramconsidered expensive.
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 prepoured. Cost $5-7 per gel.