In vitro DNA SCRaMbLE

Yi Wu, Rui-Ying Zhu, Leslie A. Mitchell, Lu Ma, Rui Liu, Meng Zhao, Bin Jia, Hui Xu, Yun-Xiang Li, Zu-Ming Yang, Yuan Ma, Xia Li, Hong Liu, Duo Liu, Wen-Hai Xiao, Xiao Zhou, Bing-Zhi Li, Ying-Jin Yuan and Jef D. Boeke ()
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Yi Wu: Tianjin University
Rui-Ying Zhu: Tianjin University
Leslie A. Mitchell: NYU Langone Health
Lu Ma: Tianjin University
Rui Liu: Tianjin University
Meng Zhao: Tianjin University
Bin Jia: Tianjin University
Hui Xu: Tianjin University
Yun-Xiang Li: Tianjin University
Zu-Ming Yang: Tianjin University
Yuan Ma: Tianjin University
Xia Li: Tianjin University
Hong Liu: Tianjin University
Duo Liu: Tianjin University
Wen-Hai Xiao: Tianjin University
Xiao Zhou: Tianjin University
Bing-Zhi Li: Tianjin University
Ying-Jin Yuan: Tianjin University
Jef D. Boeke: NYU Langone Health

Nature Communications, 2018, vol. 9, issue 1, 1-9

Abstract: Abstract The power of synthetic biology has enabled the expression of heterologous pathways in cells, as well as genome-scale synthesis projects. The complexity of biological networks makes rational de novo design a grand challenge. Introducing features that confer genetic flexibility is a powerful strategy for downstream engineering. Here we develop an in vitro method of DNA library construction based on structural variation to accomplish this goal. The “in vitro SCRaMbLE system” uses Cre recombinase mixed in a test tube with purified DNA encoding multiple loxPsym sites. Using a β-carotene pathway designed for expression in yeast as an example, we demonstrate top-down and bottom-up in vitro SCRaMbLE, enabling optimization of biosynthetic pathway flux via the rearrangement of relevant transcription units. We show that our system provides a straightforward way to correlate phenotype and genotype and is potentially amenable to biochemical optimization in ways that the in vivo system cannot achieve.

Date: 2018
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DOI: 10.1038/s41467-018-03743-6

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