Performance of DNA primers synthesized with Kilobaser

Kilobaser benchtop DNA Synthesizer machine for in-house DNA Synthesis. Microfluidic chip based. Synthesize DNA oligos, DNA primer, DNA probes in less than 2h.

How is the performance of primers synthesized by Kilobaser? This a very frequently asked question by our customers. Naturally, even if Kilobaser has good ROI regarding money and time saved, you’d still not invest in a device without good assurances that the quality will not cause problems in your workflow. To demonstrate how our device can help in various real-world applications, we conducted several experiments, publishing the results in the application note referenced in this article. We hope to provide sound quantitative insight into the quality and performance which can be expected from Kilobaser synthesized primers.

Spec-wise, the overall yield of Kilobaser is around 300 pmol with a step-wise yield of about 99,5%, which is comparable to every other manufacturer known to us. To evaluate our primers performance, we choose an experiment which uses real-time quantitative PCR and performed it twice to compare the results. Once with primers produces by Kilobaser and once with primers uses as a reference ordered from an service provider that delivers via postal service.

Situation due to CoViD-19

Billions of people on this planet live and work in disrupted conditions, due to the outbreak of SARS-CoV-2 and the necessary steps to mitigate the virus’s spread. Supply chains have become disrupted or stopped. Business needed to shut down and major restrictions in travel have become necessary.

Consequently, oligo delivery has also become unreliable, in a time where they are highly needed. Exploring the virus, SARS-CoV-2 and developing vaccines against it, is an application where custom primers are indispensable.

We believe that Kilobaser, as Express DNA machine, can help accelerate the development of efficient testing methods for the detection of SARS-CoV-2, as it ensures constant and timely availability of primers, independent of any supply disruptions

What does Kilobaser do?

Kilobaser is an Express DNA machine, a DNA synthesizer that creates ready-to-use DNA sequences right on your lab bench, within less than 2 hours. It uses an unique microfluidic chip technology paired with a handy cartridge, that enables the safe handling of the contained chemicals. As the user is never in touch with any chemicals, no special training or knowledge is required. A ready to use Kilobaser with activated cartridge, only needs a fluidic chip, a PCR vial and your desired sequence to produce DNA. It is extremely easy and straight-forward to operate Kilobaser. Oh yes, you also have to press “Start”. Check out our tutorial videos, to see how easy it is to synthesize primers by yourself.

Primers produced by the device are not affected by supply chain disruptions or postal delays and available without long waiting times. Kilobaser can help labs to work efficiently by eliminating delays. It also removes any requirements on where a lab has to be situated in order to have quick access to primers. The independence gained thus, can enable shorter creative cycles of invention as well as be a deciding factor in competitive areas where information security is the key.

We believe in independence and using time wisely and wish to give the labs of the world the tools to do their job more creatively. All life science professionals should have the ability to synthesize high quality custom DNA sequences within arm reach and not be forced to wait for their DNA order.

What is the principle of qPCR?

In Real-Time quantitative PCR (qPCR) the accumulation of DNA is monitored in real time as the reaction progresses during amplification. qPCR can be used for qualitative (the presence or absence of a sequence) and quantitative (copy number) analysis. To monitor the accumulation of DNA in real time a fluorescent dye is used to label the DNA.

The basic result of qPCR is the cycle number at which fluorescence can be detected. This value is called Quantification Cycle (Cq for short).

What have we done?

To compare the performance of Covid-19 primers from Kilobaser and Online Synthesis providers, we compare the results measured by qPCR instrument with each other. To that end, we ordered the 2019-nCoV_N1 Forward and Reverse Primer, the positive control, and a qPCR Mix from Eurofins, an online service known for its quality. Using Kilobaser we printed the same forward and the reverse primer on our lab-bench. After an automatic final deprotection/cleavage step performed by Kilobaser, DNA is eluted dry and ready-to-use.
Due to the extremely low total volume of all microfluidic channels, Kilobaser primers contain extremely low concentrations of salt. This allows us to skip any desalination steps without affecting performance, as in most applications like PCR or qPCR the remaining salts are not present in quantities where they would influence the PCR result.

In the next step we diluted DNA in Tris-EDTA (TE) buffer. The buffer keeps the DNA soluble in water and EDTA, a chelator of cations such as magnesium, protects DNA against enzymatic degradation.

Please refer to our application note for details and numerical results of the experiment.

What did we learn?

Kilobaser primers provide the same performance as primers purchased from the online synthesis service Eurofins. Kilobaser complements PCR thermocyclers and increases productivity. In a lab setup where most steps of an experiment can be completed right away, yet can not be begun until the post has arrived, Kilobaser fills a gap on every lab bench. Be independent and print high quality primers whenever you need them. Use them right away.

Time is precious. Kilobaser helps you to save a lot of precious time and cut down on hassle. Test any of your ideas right away without any delays.

NEWS – State of the art and a look to the future:

Currently Kilobaser synthesizes standard primers. However, this is just the beginning. Synthesis of modified primers and RNA primers is in the works. In principle, this would even be possible today by only exchanging our standard cartridge with our upcoming RNA- and probe- specialized reagent cartridges. In practice the necessary protocols are still being developed and optimized, as it is our goal to provide quality that you can entrust your experiments to without worry.

Expect consumables for modified primers at the end of 2020. Cartridges for RNA synthesis are scheduled for availability after mid 2021.

Stay excited!

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