Since its discovery in 1983 and quick acceptance leading to a Nobel prize in Chemistry a decade later [1], PCR and its hallmark tubes have made their way into nearly every life science lab across the country. 

While many know what PCR tubes look like, all tubes are not created equal, especially given the many manufacturers and suppliers that distribute PCR tubes across the globe. 

Below are a few tube details to be mindful of when setting up and running your own PCR experiments. Even if you’re a PCR pro, you may have never considered the subtle intricacies that make up PCR tubes. And if you have, enjoy this refresher!

PCR tubes vary from one another in few ways: plastic material, fill volume, profile, wall thickness, and clarity.  

The vast majority of PCR tubes are made from polypropylene (PP) plastic due to its inertness and excellent heat transfer capacity. That said, some PCR tube manufacturers opt instead for polyethylene (PE), but these are often intended for specific instruments, and therefore are not as broadly applicable to the wide variety of available thermocyclers. 

Fill volumes represent the maximum reaction volume in a PCR tube where appropriate thermocycling and PCR amplification can still occur. The traditional PCR tube holds 200µL, but 500µL and 100µL variants are often available as well. Different sized tubes may require PCR blocks able to fit these tubes properly and ensure the reaction mixture receives adequate and uniform heating.

Similarly, some PCR tubes have different heights, a characteristic called profile. Generally, traditional and low-profile PCR tubes have the same fill volume but differ with respect to the air volume above the reaction solution. While minimized air space in low profile tubes can help reduce evaporation and increase thermal conductivity, these tubes are only intended for specific thermocyclers.

PCR tube wall thickness must be uniform to enable consistent heat transfers across the tube. Overall, thin or ultrathin PCR tube walls are ideal, since thinner plastic improves thermal exchange with the block, leading to more effective PCR reaction cycling.

PCR tube clarity is an important characteristic for fluorescence readings during qPCR experimentation. Importantly, you’ll need optically clear caps and white tubes to enable maximum fluorescent signal detection, since this combination better directs fluorescence emission to the reader.

You should also decide whether you want individual tubes, tube strips, or both. Individual tubes are great for small reaction numbers, but their handling becomes more laborious and tedious as sample numbers expand, especially if you need to label and track each tube individually. 

Tube strips are great for managing larger numbers of samples but make individualized sample management more difficult. If you do choose tube strips, you can choose either those with or without caps directly attached. Since some thermocyclers require either domed or flat caps for optimum fit and optically clear caps are essential for qPCR, tubes without caps come with benefit of cap interchangeability to accommodate any setup. 

Attached caps are a bit more user friendly to apply since you can click each tube cap individually. Additionally, it’s easy to manually cut tubes from a strip when caps are attached directly. 

PCR is a highly sensitive technique, so quality in your PCR plastics can end up really impacting your results. For this reason, Thermo Fisher Scientific makes its own PCR plastics with a commitment to the highest-quality PCR manufacturing.

Given the risks contamination poses to PCR success, it is essential that you confirm that your PCR tube supplier guarantees that their materials are DNA/RNA and nuclease free. Contaminating DNA/RNA and nucleases can result in false positives and false negatives respectively, each creating confusion and frustration for your work. 

Less well known is the importance of the plastic itself. If your PCRs are routinely failing and you’ve ruled out your reagents, it is possible that your tube plastic is leaching inhibitory chemicals [2]. Additionally, PCR tubes can also leach light-absorbing materials that interfere with spectrophotometric analysis [3]. For these reasons, it’s often best to work with suppliers who use medical or molecular-grade virgin plastic, since freshly synthesized PP is much less likely to include unexpected chemical leachates. 

Some PCR users report issues with tube melting or deformation, which can also be an indicator of poor plastic quality or manufacturing complications. Should this happen, first try switching to tubes from separate lot numbers to test the possibility of fluke plastic manufacturing issues. Should the issue repeat, it’s probably time to switch to a more widely used and well-known provider. 

That said, remember that PCR tube deformation can also be an issue of the tubes not correctly fitting your PCR block. If you need help confirming your tubes are compatible with the thermocycler you use, check out our PCR Plastic Selection Tool!

1. The Nobel Prize in Chemistry 1993. The Nobel Prize (2021): ePub.  
2. G Reid McDonald, et al. (2008) Bioactive contaminants leach from disposable laboratory plasticware. Science. Science, 322(5903): 917.   
3. Lewis LK, Robson M, Vecherkina Y, Ji C, Beall G (2010). Interference with spectrophotometric analysis of nucleic acids and proteins by leaching of chemicals from plastic tubes. Biotechniques, 48(4):297-302.