DNA synthesis — a technical primer
An engineering, not a biology problem
Written by Compound’s Shelby Newsad and Breakout Ventures’ Nima Ronaghi
TL;DR
Democratizing access to cheap, readily available, and long DNA will facilitate an explosion in the bioeconomy; companies that synthesize DNA at a low cost, while still providing high accuracy and fast turnaround time, will create tremendous value. Historically, higher turnaround times, improved accuracy, and precipitous cost decreases in DNA synthesis have been made possible through engineering advances — we predict that this trend will continue in the future.
Context
DNA synthesis is a primary bottleneck in the near-future bioeconomy. Without rapid and high fidelity DNA writing technology, the promise of DNA storage, de novo organisms, and gene therapy cannot be realized. Where DNA sequencing has decreased by six orders of magnitude (in light of the $100 Ultima genome, although there is some skepticism). DNA synthesis has lagged behind, only decreasing in cost by 3–4 orders of magnitude. (The cost of DNA synthesis varies depending on the method with a trade-off in cost an accuracy — Table 1.) This is due to the comparative difficulty in having a template (sequencing) or not (synthesis). De novo DNA synthesis first requires the synthesis of a single strand of DNA which can be conducted through phosphoramidite chemistry or template-free DNA synthesis enzymes. Both techniques require the sequential addition of nucleotides.
The DNA synthesis market first took off when Twist was able to miniaturize the phosphoramidite chemistry on a silicon wafer (chronicled here). Twist’s current technology allows for the parallel synthesis of 9,500+ strands of DNA. Twist’s success hinges upon parallelization which drives down cost, improves quality, and increases length of constructs (and turnaround time if you’re a DNA service company). However, phosphoramidite chemistry is still limited in sequence length (200-mers), accuracy and yield, due to imperfect nucleotide coupling efficiency, imperfect protection/deprotection chemistry, and depurination occurring as a natural side reaction. That being said, there are depurination-resistant methods and reagents which could theoretically allow for longer sequence lengths with phosphoramidite chemistry.
