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How to avoid cross-contamination in qPCR

To avoid cross-contamination in qPCR, key practices include: separating pre- and post-amplification areas with dedicated equipment, using a unidirectional workflow, including a “no template control” in each run, properly cleaning work surfaces with ethanol, and utilizing specialized reagents like UDG (uracil DNA glycosylase) to prevent carryover contamination; essentially, maintaining a clean workspace with distinct areas for different stages of the qPCR process and using appropriate techniques to prevent contamination from amplified DNA fragments. 

Key points to remember:

  • Dedicated spaces: Designate separate areas for sample preparation, PCR setup, and post-PCR analysis, ideally with different rooms and equipment for each stage. 
  • One-way workflow: Always move from pre-amplification to post-amplification areas, never going backwards to avoid potential contamination transfer. 
  • Cleanliness: Thoroughly clean all work surfaces and equipment with 70% ethanol before and after each experiment, especially after spills. 
  • Pipette technique: Use fresh, filtered pipette tips for each sample and avoid touching the inside of the tube with the tip. 
  • Negative controls: Include a “no template control” (NTC) in every qPCR run to monitor for potential contamination. 
  • UDG enzyme: Consider using a qPCR master mix containing UDG enzyme which helps degrade any carryover DNA from previous reactions. 
  • PPE: Wear appropriate personal protective equipment (PPE) like gloves and lab coats, changing them regularly when moving between different areas.

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