Hi Reader, ever since COVID, we have all heard about PCRs.
The Polymerase Chain Reaction, which elongates DNA or RNA chains.
As it is a standard method used in almost every Life-Science laboratory, it is a topic we have to cover.
Here is everything from the environmental impacts of PCR to how we can make it more sustainable:
Today's Lesson: Making PCRs More Sustainable
How we can save resources, time, and money.
Number Of The Day
A single PCR run requires about 0.135 kWh (based on the Eppendorf Mastercycler X40). In comparison, a -70°C freezer consumes about 6 kWh per day. With reference to material use, Celis et al. found that one wastes about 23.44 g of plastic waste per sample when conducting RT-PCR for COVID testing (excluding the plastic used for the initial home smear tests). So, can we reduce these impacts?
0.135
Making PCRs more sustainable
The Polymerase Chain Reaction was developed in 1983 by Kary Mullis - not in academic research but at a biotechnology company.
He was awarded the Nobel Prize in Chemistry in 1993, ten years later, together with Michael Smith who worked on site-directed mutagenesis.
Although little has changed since then, there are a few optimizations that few consider:
Saving Plastic Waste
Every PCR consists of water + nucleotides + forward and reverse primers + DNA/RNA template + polymerase + buffer.
To save plastic waste, we can optimize pipetting orders by:
If you have replicates, starting with water, then the template, keeping the same tip to distribute it among tubes/plates
Preparing a master mix – using the same pipette tip to add the final component and distributing the mix.
If possible, pipetting components (like the Master Mix or even the template DNA) at the wall of the tube/plate and spinning it down – allowing you to reuse the same tip.
If you have only one or two templates but you prepare several PCRs for it, you can start by pipetting water and DNA first. If possible, pipette the master mix on the wall and spin it down. However, if you have only one replicate of several templates but the same primers for all, invert the order and prepare the master including the water first.
= By doing so, you can save up to 38% plastic waste according to our estimate.
I have summarized some more tips on pipetting in our free Slack channel for you – in the end it is all about being creative to find what fits you.
Optimizing Your Runs
PCR cycles have barely changed over the years.
However, a paper released last year challenged this paradigm. Pedlar et al. tested a shortened protocol featuring 30 cycles of:
5 s denaturation
25 s annealing
25 s extension
They used a 1466 bp fragment from the 16S rRNA gene and verified success through downstream fluorescence readout.
As a result, they reduced program duration by 46% and consumed 50% less electricity!
Holding Temperatures
A widely known practice is to increase holding temperatures.
Since most cyclers default to holding DNA at 4°C, it’s feasible to raise this to 12°C, with many labs going to 14°C or even 16°C.
Although the Master X50s is larger and faster (with a steeper ramp rate), the instrument is equipped with an efficient heating and cooling system, resulting in 15% lower energy consumption per standardized run. Daily consumption is based on four standard runs, with the rest of the 8-hour day spent idle.
Although dependent on time, one can estimate that holding at lower temperatures can easily make up one third of energy consumption.
Based on our collaboration with Eppendorf, they shared that increasing the holding temperature from 4°C to 10°C saves between 30–45% energy depending on the model.
And for all who doubt – yes, it is save for a couple of hours. Probably even longer, but best practices clearly recommend processing or freezing your DNA afterwards.
Choosing the Right Model
Of course, various PCR cyclers exist.
When it comes to sustainability, only two manufacturers have ACT labels available for their PCR cyclers:
Eppendorf and Roche.
The Eppendorf Mastercycler X40 has an average energy consumption of about 0.7 kWh/day (assuming 4 standard runs and idle time).
The Roche LightCycler Pro uses about 2.8 kWh/day — but it also supports 384-well plates and has other additional features.
While Eppendorf’s models are mostly made of metals and electrical components (about 70% of their weight), one can hope these parts are mostly recycled if sent to proper waste treatment facilities.
Applying The Knowledge
As always, go with the changes you're comfortable with.
Especially for “test” runs — like checking if a primer works or if an enzymatic cut happened — optimizing cycle lengths and smart pipetting strategies can really pay off to save you time.
Of course, time and plastic savings could be higher - if you e.g., downscale or optimize your pipetting order to your design respectively.
Moreover, changing holding temperatures not only saves energy but also reduces condensation and lowers equipment wear. This is an argument that certainly can be useful when trying to convince superiors.
Also worth noting: idle PCR cyclers still consume 10–12 Wh — so turn them off if not in use. Here again, saving energy and increasing lifetime.
Upcoming Lesson:
How To Measure Energy Consumption
How We Feel Today
References
Celis, J. E. et al., Plastic residues produced with confirmatory testing for COVID-19: Classification, quantification, fate, and impacts on human health. 2021. Science of The Total Environment, 760:144167. doi:10.1016/j.scitotenv.2020.144167
Pedlar, M. et al., Amplifying PCR productivity and environmental sustainability through shortened cycling protocols. 2024. Biochimie, 221:60–64. doi:10.1016/j.biochi.2024.01.013
Liu, W. et al., Recycling of Polymerase Chain Reaction (PCR) Kits. 2023. ACS Sustainable Chemistry & Engineering, 11(14):5524–5536. doi:10.1021/acssuschemeng.2c07309
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