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Section 5 Troubleshooting Guide
Problem
Cause
Solution
Bands sharp but not enough bands
seen
Gel agarose percentage too high
Incomplete digestion
Decrease agarose percentage.
Review enzyme activity, digest
further.
Band smearing and streaking
Agarose has improper endosmosis
Salt concentration in sample too high
Excessive power and heating
Sample spilled out of well
Incomplete
digestion,
nuclease
contamination, bad enzyme
Sample wells cast through the gel.
Sample leaks along bottom of
running surface
Consult Cleaver Scientific about
agarose.
Reduce salt concentration to ≤0.1M.
Reduce voltage. See electrophoresis
instructions.
Apply sample carefully. Increase gel
thickness for large sample volumes.
Adjust comb height.
Heat
sample.
Review
enzyme
activity. Digest sample further.
Comb should be placed to 1 to 2 mm
above the base of the running
surface.
Curved line or distortion of bands
Bubbles in sample wells
Remove
bubbles
prior
to
electrophoresis.
Curved bands, smiles
Sample overload
Reduce load.
Differential relative mobilities
Sample spilled out of wells
Unit not leveled
Samples should have proper density.
Apply carefully.
Level unit. Use a steady work bench.
Gels crack
Too high voltage gradient, especially
with low melting temperature
agarose or low gel strength gels
Reduce voltage. Run gel at lower
temperature.
High MW bands sharp; low MW
bands smeared
Gel agarose percentage too low
Increase agarose percentage. Switch
to polyacrylamide.
Ragged bands
Sample density incorrect
Sample well deformed
Excessive power or heating
See sample application instructions.
Carefully remove comb, especially
from soft gels. Make sure gel has
solidified.
Cooling soft gels aids in comb
removal.
Reduce voltage. See electrophoresis
instructions.
Slanted lanes (bands)
Gel not fully solidified
Comb warped or at an angle
Gel to solidify for at least 30-45min.
Check alignment of comb.
