15/11/2018
Page 13
Troubleshooting
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 levelled
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.
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