Applied Biosystems 3500 User Manual

Symptom
Possible cause Action
No current. Bubble(s) present in the lower
polymer block and/or the array
and/or channels.
Pause the run and inspect for
bubbles in the tubing connectors. Run
the Remove Bubbles wizard.
Elevated current. Degraded polymer. Run the Replenish Polymer wizard.
Arcing in the lower polymer block. Inspect the lower polymer block for
discoloration or damage. Contact
Thermo Fisher Scientific.
Fluctuating current. Bubble in polymer block. Pause run and inspect for bubbles
hidden in the tubing connectors. Run
the Remove Bubbles wizard.
Slow leak Check polymer blocks for leaks.
Tighten the connectors and array
locking lever.
Not enough buffer in ABC. Ensure that the buffer is filled up to
the fill line. See “Check buffer fill
levels“ on page 34.
Arcing Check for moisture in and around the
septa, the CBC, the oven, and the
autosampler. Wipe condensation.
Poor performance of capillary array
used for fewer than 100 runs.
Poor quality samples, possible
cleanup problems.
Desalt samples.
Improperly stored formamide. Prepare fresh Hi‑Di
™
Formamide (see
“Hi‑Di
™
Formamide“ on page 22 for
storage conditions) for sample
preparation.
Leak in system. Tighten the connectors and array
locking lever.
Migration time becomes
progressively slower.
Leak in system. Tighten the connectors and array
locking lever.
Improper filling of the sys
tem with
polymer.
Polymer delivery pump may need to
be serviced. If the issue persists,
contact Thermo Fisher Scientific.
Migration time becomes
progressively faster.
Buffer valve leakage. Ensure the buffer-pin valve is closed
correctly.
Extra peaks in the electropherogram. Data off scale. Dilute the sample and re-inject the
sample.
Possible contaminant in sample. Re-amplify the DNA.
Sample re-naturation. Heat-denature the sample in properly
stored formamide (see “Hi‑Di
™
Formamide“ on page 22 for storage
conditions) and immediately place on
ice.
Appendix A Troubleshoot
Data/electropherogram troubleshooting
A
266
3500/3500xL Genetic Analyzer User Guide—Data Collection Software v3.1

Applied Biosystems 3500 Specifications

General

Number of capillaries	8
Capillary Length	50 cm
Laser	Solid-state laser
Instrument Type	Capillary electrophoresis system
Technology	Capillary Electrophoresis (CE)
Weight	95 kg
Power Requirements	100–240 V