Fast, Cost-Effective and High-Throughput Solutions for DNA Assembly

The development of next-generation therapeutics, pharmaceuticals and biofuels, among other life sciences products, hinges on fast and efficient DNA assembly. But the genome is a messy tome, comprised of thousands of genetic fragments. Building these large molecular assemblies using the synthetic biology tools is an involved endeavor with complex and error-prone workflows.

Echo Liquid Handlers, from Beckman Coulter Life Sciences, provide customers with a DNA assembly solution that reduces costs, runtimes and reaction volumes without sacrificing data quality. From fragment pooling and gene assembly to colony arraying and functional testing, Echo Liquid Handlers improve critical steps in the workflow, offering a fast, high-throughput and cost-effective solution technology.

“Echo is an extremely fast instrument…a significant savings in terms of time. We’ve been able to compress pipelines that take about 12 hours to about 3 hours.”
–Dr. Sunil Chandran, Amyris Biotechnologies

Gene Synthesis Workflow

Figure 1- A typical gene synthesis workflow

Streamlining the workflow

The Echo 525 Acoustic Liquid Handler streamlines the design-build-test-learn cycle associated with DNA assembly through a tip-less, non-contact solution. Using acoustic ejection technology, the Echo 525 dispenses volumes as low as 25 nL accurately and precisely, with a fast flow rate of up to 6 µL/sec.

Using dynamic fluid analysis technology, the Echo can then adjust transfer parameters in real-time for a variety of samples, including DNA, RNA, enzymes and master mixes in glycerol storage solution, without requiring any user calibration. Performing precise, accurate and fast liquid transfers from any source plate well to any destination plate well is now easier than ever.

For scientists and researchers working in high-throughput or discovery phase these features will make a big difference in being able to use a flexible and user-friendly technology that enables fast and easy reaction set ups.

Figure 2- A) Echo 525 and 650 Series Liquid Handlers, B) Acoustic droplet ejection - The transducer is positioned below the source microplate well and emits focused sound energy repeatably to the meniscus of the fluid to be transferred. A stream of 2.5 or 25 nL droplets (model dependent) is reliably ejected into a well of an inverted destination microplate

Improving through miniaturization

Big things have small beginnings. And that’s true when it comes to the Echo 525, which improves efficiency through miniaturization.

Echo Liquid Handlers were shown to successfully reduce gene assembly volume sizes by 40-fold, from 20 µL to 500 nL. Additionally, Echo customers have reported that when using the device for qPCR, they reduced reaction volumes by 10 times, resulting in a reported eight-fold decrease in costs per reaction sample.

Reducing Reaction Costs while Improving Assembly Efficiency with Miniaturization

Figure 3- Gibson and Golden Gate Assembly: Cost-effectiveness and assembly efficiency comparison of different reaction volumes.¹

“We envision that acoustic dispensing will become an instrumental technology in synthetic biology.”
Paulina Kanigowska, J. Lab Autom., 2016 Feb;21(1):49-56

Low-Cost, Highly Efficient NGS Library Preparation

Figure 4- Echo Liquid Handlers offer 40X cost-savings in an NEBuilder workflow, and 10X cost-savings in a next-generation sequencing (NGS) library prep for validation of the assembled genes.

As the cost of sequencing has gone down, the cost of library prep is becoming the bottleneck in many high-throughput NGS applications, including NGS methods used for validation of assembled genes. One way to reduce library prep cost is to reduce reaction volumes. In a case study by one of the Echo users, Echo Liquid Handlers not only enabled 40X reduction in assembly reaction volume and cost but also offered a 10X cost savings.

Up to 82% Increase in Speed of Gene Assemblies and NGS Validation Steps

Figure 5- The Echo Liquid Handlers enabling over 82% saving on time that it takes to set up and validate the gene assemblies, compared to traditional liquid handlers.

The Echo can rapidly pool DNA fragments for gene assembly and normalization and pooling of NGS libraries for sequencing, with each transfer taking less than a second. This provides time savings of up to 82% in a gene assembly and validation process, while providing superior %CV of the pooled libraries through accurate and precise transfers.

For a deeper dive into how Echo Liquid Handlers, paired with Integrated DNA Technologies (IDT) gene fragments provided in the Echo qualified source plates, can improve DNA assembly workflows, watch the webinar “Fast, Cost-Effective and High-Throughput Solutions for DNA Assembly.”

References

1. Kanigowska P, Shen Y, Zheng Y, Rosser S, Cai Y. Smart DNA Fabrication Using Sound Waves: Applying Acoustic Dispensing Technologies to Synthetic Biology. J Lab Autom. 2016;21(1):49-56. doi:10.1177/2211068215593754