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Amplified DNA Product Separation for Forensic Analysts


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Troubleshooting Guide


Possible Cause


Poor mobility and reproducibility

Temperature fluctuation

  • Check instrument oven
  • Check environment temperature

Blocked, dirty capillary

Change capillary

Sample-wall interaction

Rinse capillary with polymer

Ion depletion of buffers

Replace buffers

Buffer siphoning

Buffer reservoir levels not equal

Equalize buffer levels

Poor sensitivity

Not enough amplified product in sample

Reamplify or add more amplified product

Bubble in sample tube, capillary exposed to bubble


Poor laser power

Service call, possible laser replacement

Ion competition during electrokinetic injection

  • Check quality of formamide
  • Compare results of sample to positive control included in kit - if okay, then evaluate extraction and sample preparation

Poor matrix

Rerun matrix

Gradual change in current

Different cathode/anode buffers and/or concentration

Confirm buffers

Current fluctuations

Bubbles in the system

Conduct a visual check for bubbles and clear by flushing with fresh polymer.

No current

Plugged capillary

  • Flush with polymer
  • Replace capillary

Wrong buffer

Confirm buffers

Noisy baseline

Poor matrix

Rerun matrix

Flat baseline

Capillary not aligned in detector window

Realign capillary

No voltage

  • Confirm voltage settings
  • Ensure capillary ends are immersed in buffer

Sample not injected

Confirm the following:

  • Sample in vial
  • Sample is thoroughly mixed with formamide and is not on the side of the tube
  • Capillary end in sample solution
  • Injection time

Laser not functioning

Service call, possible laser replacement

Clogged capillary

  • Replenish with fresh polymer
  • Replace capillary

Electrical arcing

Buffer spill in high voltage areas

Clean autosampler tray with distilled water and wipe dry

Poor peak shape

Incorrect current causes:

peak distortion

tailing [low current]

Replace buffer

Capillary failure

  • Replenish capillary with fresh polymer
  • Replace capillary

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