Guides

The Hitchhikers guide to DNA outsourcing – 6 does and dont’s to unblock the bottleneck

The Biofoundry Team

With an industry focussed on lowering the price of DNA, we are missing other important metrics underpinning success in Synthetic Biology. Of these, turnaround time and reliability are the most stubborn problems blocking progress. We explain what you can do to improve success in DNA outsourcing.

For much of its history, the exponential decline in the cost of DNA has been held as the central metric of progress in Synthetic Biology. 

Often compared to Moore’s law, the dropping price of DNA has sparked a wealth of startups and new research. 

But cost is an incomplete metric that hides many challenges. 

That’s because, as many DNA customers understand; reliability and turnaround have become the major limits to discovery.

In this piece by Gingko the picture is clearly painted: for nearly all suppliers, turnaround time is highly unpredictable and rarely fast enough to make outsourcing a viable part of the development cycle. 

 

Turnaround time for most providers is highly unpredictable and rarely fast enough to make outsourcing a viable part of the development cycle.

 

A mature synbio market depends on an efficient supply chain like any other. 

Which means DNA must not only be cheap but as reliable to source as the chips that sparked the digital revolution.

For four years, we’ve been building a reliable DNA pipeline at Doulix to support advanced research. And in this time, we’ve learnt there’s a lot you can do to improve your chances of success.

So, to help you unblock your synthesis bottleneck, our resident experts Sota & Florian share their advice for faster, more successful DNA outsourcing.

doulix DNA studio in action
A major burden of outsourcing your DNA is making sure it is technically ready to be synthesised.
Careful of complexity

This will be familiar one but it is still the most common problem we see. Repeats, secondary structures and high GC content cause an array of problems during synthesis and assembly.

Simplifying complexity in the design stage with optimization tools can have a big impact on success and turnaround. 

 

Check your primers

Make sure to avoid stable secondary structures, self/hetero dimers and other fiddly details like having C or G in the first position on the 3’ end, or that the first 6-10 nucleotides from 3’ to 5’ end are not repeated elsewhere.

 

Consider toxicity

Always consider toxicity created by your sequence. It could be from a translated CDS product or a regulatory element but either way, it is a problem. This can be an issue with poorly characterised public parts as an overly strong promoter can mean delays due to trialling multiple cloning methods and screening hundreds of colonies.

 

Plan for failure

When working on custom builds, whereby a successful protocol has not yet been proven, we will adapt sequences to allow for contingencies. We’ll add restriction sites to linearize a plasmid as a backbone in case PCR approaches fail; we’ll design overlapping regions to be compatible with multiple assembly methods or design multiple primer pairs to increase resolution for colony screening PCR.

 

Regulate

Ensure unwanted gene expression is suppressed in the cloning strain to avoid unnecessary metabolic burden and selection of deleterious mutants. Check your promoters are regulated in the cloning host and ensure proper terminators to prevent accidental read-through.

 

Finally, treat it like a relationship

Working in a Synbio laboratory is like a relationship; it needs constant attention. Or else, the moment you get complacent is the moment it all goes wrong. What’s the moral? Whether you’re outsourcing or staying in house, never take your protocols and tools for granted.