Contamination of samples and reagents can be a major issue when extracting and amplifying DNA – especially outside of traditional laboratory environments. But with the right precautions, it’s possible to work cleanly, minimise contamination, and manage any issues that do occur.
In this post, we share 10 essential tips and tricks to help you avoid contamination during DNA workflows. These are particularly useful for portable, field-based, or temporary setups.
What Is DNA Contamination?
Contamination is any foreign material that ends up in your samples, reagents, or equipment – potentially damaging them or interfering with your results. There are three main types:
1. Environmental Contamination
This includes dust, spores (fungal or bacterial), fingerprints, sneezes, and other airborne or contact-based contaminants. If you’re doing sensitive work, it’s crucial to keep your environment as clean as possible.
2. PCR Product Contamination
This involves concentrated DNA from previous PCR runs – either yours or someone else’s. Trace amounts left on pipettes or surfaces can lead to false positives by re-amplifying old DNA instead of the intended sample.
3. Cross-Contamination
DNA, reagents, or samples accidentally contaminating each other. This can cause failed experiments or incorrect results, especially in multiplex or comparative setups.
10 Practical Tips to Avoid Contamination
1. Always Wear Gloves
Wear gloves whenever handling samples or reagents. Change gloves regularly – especially if they get dirty or you’re switching tasks. You can clean more durable gloves with bleach wipes if needed. If you opt not to wear gloves, only do so in low-risk steps without health and safety concerns.
2. Use New Pipette Tips
Never reuse tips between different reagents or samples. If a tip touches anything it shouldn’t, discard it immediately. For sensitive work, consider using filter tips, which prevent aerosol contamination from entering your pipette.
3. Treat Your Pipette Carefully
PCR products can contaminate the inside or outside of your pipette. Ideally, use a dedicated pipette for PCR products. Regularly clean pipettes with bleach wipes and store them in sealed containers. You can also disassemble the pipette and soak the shaft in dilute bleach (e.g. 10%) for 15 minutes, then wipe it dry thoroughly.
4. Create a Clean Working Space
The cleaner your workspace, the better your results. You can use:
- A wipe-down plastic tablecloth
- A plastic tray cleaned with 10% bleach solution
- A new sheet of aluminium foil or clean paper
Make sure anything used as a surface is clean or from inside a sealed pack. Discard these after use.
5. Keep Samples Separate
Avoid contact between your samples, PCR products, and the environment. Work on each sample on a separate surface (foil or paper), then dispose of that surface. Store samples in bags or boxes that can be wiped clean. Keep tubes or containers separated to prevent cross-contamination.
6. Use Clean Sampling Tools
Sterilise any tools between uses. For example:
- Use new razor blades or disposable scalpels.
- Soak reusable tools (e.g. tweezers or scissors) in 10% bleach for 5–10 minutes, then rinse and wipe with clean paper towel.
7. Be Careful with Your Gel Tank and Buffer
Gel tanks and running buffer can easily become contaminated with PCR product. Avoid pipetting DNA into the buffer or overrunning your gel. Always:
- Handle gel and buffer with care.
- Change gloves after touching used gel tanks.
- Dispose of used buffer in a safe location (not your kitchen sink!). Use a disposable bottle or pour it down the toilet if needed.
- Wipe the outside of gel tanks with bleach before storing.
8. Separate Workflow Steps by Time or Space
Ideally, perform DNA extraction and PCR setup in a different space from where you run gels. Use separate pipettes and tools if possible.
If space is limited, separate steps by time – clean thoroughly between stages. For example:
- Use a clean area for extraction.
- After gel electrophoresis, wipe down your tools and surfaces with bleach, leave for 15 minutes, then wipe off thoroughly.
9. Aliquot Reagents into Small Volumes
Reagent contamination is costly. To minimise waste:
- Divide reagents into smaller aliquots and freeze them.
- If contamination occurs, you only lose a small portion, not your entire supply.
10. When in Doubt, Clean It
If you suspect something might be contaminated, clean it or set it aside until you can. This might mean:
- Changing gloves or pipette tips
- Replacing foil or paper surfaces
- Cleaning tools or surfaces with bleach
Make cleaning part of your end-of-day routine. This way, you’ll start each experiment fresh and avoid lingering issues.
Final Thoughts
Sterile practice is all about good judgment. You don’t need to be perfect, but developing consistent habits makes a huge difference – especially in portable, DIY, or resource-limited settings.
Contamination is inevitable at some point, but with these tips, you’ll be better prepared to prevent it, and deal with it quickly when it arises.
If you’re working on DNA extraction and amplification outside of a traditional lab, we hope these tips help you get cleaner, more reliable results.
Have your own contamination tips or questions? Let us know! We’d love to hear from you.
