PCR Aerosol Contamination: Causes, Consequences and Solutions

April 28, 2023

What is PCR aerosol contamination?

Aerosol contamination in PCR amplification refers to DNA/RNA aerosol contamination, which is a type of airborne contamination that can occur in the laboratory. For example, during centrifugation, rapid shaking of reaction tubes, repetitive opening and closing of caps of reaction tubes and repetitive pipetting, minute droplets of nucleic acids escape into the air and collide to form what we commonly refer to as nucleic acid aerosols.

There are multiple causes of PCR aerosol contamination, the most common of which are as follows:

  • Inadequate laboratory conditions, such as those without positive or negative pressure systems

  • Inappropriate experimental procedures

  • Proteinase K, blood components, and other inhibitors or interferers present in the sample or reagent

Contamination can also occur during the collection, delivery, storage, or extraction of nucleic acids.


How to identify PCR aerosol contamination?

If system contamination and sample cross-contamination have been ruled out, but the target band still amplifies using deionized water as the template, there is a high likelihood of aerosol contamination. In addition, aerosol contaminations tend to amplify bands ranging between 80 to 500bp.

How to resolve aerosol contamination?

The risk of aerosol contamination can be reduced in two ways: first, by ensuring that PCR reactions are performed in a sterile environment, and second, by avoiding generating aerosols during handling and pipetting.

1. Prevent PCR contamination:

  • Carry out PCR experiments in an environment with constant air pressure.

  • Use fresh reagents and consumables, such as primers, enzymes, deionized water, and EP tubes.

  • Maintain a clean work area and instruments.

  • Use more stringent amplification conditions, such as the landing PCR protocol (Touch Down, or TD for short) for amplification. In TD, the annealing temperature is increased incrementally at each additional amplification cycle, making the TD program highly effective in addressing contamination, non-specific amplification, primer dimerization, and other  issues.

2. Keep the laboratory environment clean:

Maintain good laboratory practice: Wipe the bench and pipettes with 75% ethanol before performing PCR experiments. Avoid violent shaking and gently open and close EP tubes during DNA extraction, primer preparation, and configuration. Clean the table with 75% ethanol at least twice in case of sample splashing.

With our extensive genotyping experience, we have compiled a "Mouse Genotyping Instruction Booklet" that explains our practice and troubleshooting strategies in great detail. Please get in touch with us for more information: sales@gempharmatech.us