DNA-BOT: A low-cost, automated DNA assembly platform for synthetic biology

Abstract

Multi-part DNA assembly is the physical starting point for many projects in Synthetic and Molecular Biology. The ability to explore a genetic design space by building extensive libraries of DNA constructs is essential for creating programmed biological systems that perform the desired functions. With multiple DNA assembly methods and standards adopted in the Synthetic Biology community, automation of the DNA assembly process has received serious attention in recent years. Importantly, automating DNA assembly enables larger builds using less researcher time, increasing the accessible design space.However, these benefits currently incur high costs for both equipment and consumables. Here, we address this limitation by introducing low-cost DNA assembly with BASIC on OpenTrons (DNA-BOT).For this purpose, we developed an open-source software package dnabot (https://github.com/BASIC-DNA-ASSEMBLY/dnabot). We demonstrate the performance of DNA-BOT by simultaneously assembling 88 constructs composed of 10 genetic parts, exploring the promoter, ribosome binding site (RBS) and gene order design space for a 3-gene operon. All 88 constructs were assembled with high accuracy, at a cost of $1.50 -$5.50 per construct. This illustrates the efficiency, accuracy and affordability of DNA-BOT making it accessible for most labs and democratising automated DNA assembly.

Unlocking the efficiency of genomics laboratories with robotic liquid-handling

“…While it performs only the most basic pipetting operations, it claims to do so at gold-standard accuracy. At the periphery of liquid-handling for genomics, there are other DIY robots like the EvoBot and PlasmoTron, used for chemical life research and parasite culture respectively [57,58]. This shows a real momentum towards developing accessible solutions for laboratory automation in the life sciences and is an indication of an endeavor that will continue growing.…”

“…Liquid-handling automation is already finding its place in various aspects of life sciences. Be it in microbiology [59], synthetic biology [60][61][62], endocrinology [63], or genetics [58,[64][65][66], laboratory biologists are increasingly trusting automated liquid handling workstations to streamline their protocols. Genomics laboratories at prominent institutions have also already dipped their feet in liquid-handling automation, be it for gene expression, NGS, or third-generation sequencing for a number of diseases [67][68][69][70][71][72][73][74][75][76][77][78][79][80][81][82][83].…”

Biological Materials: The Next Frontier for Cell-Free Synthetic Biology

“…Co-ordinated efforts toward improving inter-laboratory data reproducibility, standardizing experimental metrology and an emphasis on industrially scalable biotechnology are also driving the adoption of automation in synthetic biology workflows (Kelly et al, 2009;Beal et al, 2016Beal et al, , 2018ade Lorenzo and Schmidt, 2018;Carbonell et al, 2019;Exley et al, 2019). In a broader sense, automation is also becoming more accessible through reductions in gene synthesis costs (Carlson, 2014), advancements in automated DNA assembly protocols (Kanigowska et al, 2016;Rajakumar et al, 2019;Storch et al, 2019;Walsh et al, 2019), rapid mass spectrometry of complex biological samples (Gowers et al, 2019;Miguez et al, 2019;O'Kane et al, 2019) and through the emergence of academic biofoundries (Chambers et al, 2016;Hillson et al, 2019).…”

EvoBot: An Open-Source, Modular, Liquid Handling Robot for Scientific Experiments

“…Commercial liquid handling robots are often employed in biochemical laboratories in order to automate specific, repetitive tasks. Most commercial robots use the same technology as for manual liquid handling, air displacement pipettes or syringes, while a few others use positive displacement pipettes or non-contact dispensing methods; see [1] for a useful overview and [2][3][4] for recent applications of commercial robots in biochemical laboratories. For these robots, reliability, performance, and precision are of high priority, and typically, less priority is given to their flexibility and extendibility.…”