Section 6
Troubleshooting
Horizontal System
6-1
Thermo Scientific
Problem
Solution
Agarose leaks into chamber
when casting the gel
Check to see if the gasket is correctly seated in groove and
even all the way around. Remove gasket and reseat by smooth-
ing out gently with your thumb from one end to the other.
Gasket material may have a tendency to absorb salts from the
running buffer. After each use, rinse the end gates under warm
running water to bring back spongelike consistence of the gas-
ket material. Gaskets may eventually become brittle with fre-
quent use. Contact Technical Services to purchase replacement
gaskets.
Bands seem to be running at
an angle.
Check to be sure that the unit is properly leveled for casting
and running the gel by using the thumbscrews on the base.
Thumbscrews should be adjusted until the bubble in the level
lines up with the levels center circle. Always center the gel
tray holder on the platform and cool the agarose to below 60°
before pouring to avoid warping the UVT gel tray (s).
Samples seem to be running
unevenly in certain areas.
Check that the platinum electrode wire is intact running flat
and evenly across the outer corners and up the side to the
junction of the banana plug area. This problem could also be
caused by regular casting with very hot agarose gel (>60° )
which may damage the gel tray over time. Always cool the
melted agarose to below 60o before casting to avoid warping
the UVT gel tray (s). Warping the UVT gel tray will cause all
subsequent gels to be cast unevenly.
Samples do not band sharply
and appear diffuse in the gel.
Gels should be no more than 5mm thick and allowed to
solidify completely before running. For standard agarose, this
would be about 30 minutes, if low melting point agarose is
used, it may be necessary to completely solidify gels at a
cooler temperature in the refrigerator or cold room. Gels
should be submerged in 3-5mm of buffer to avoid gel dry out,
but excess buffer >5mm can cause decreased DNA mobility
and band distortion.
