Automated Platform for the Plasmid Construction Process

Nava, Alberto A.; Fear, Anna Lisa; Lee, Namil; Mellinger, Peter; Lan, Guangxu; McCauley, Joshua; Tan, Stephen; Kaplan, Nurgul; Goyal, Garima; Coates, R. Cameron; Roberts, Jacob; Johnson, Zahmiria; Hu, Romina; Wu, Bryan; Ahn, Jared; Kim, Woojoo E.; Wan, Yao; Yin, Kevin; Hillson, Nathan; Haushalter, Robert W.; Keasling, Jay D.

doi:10.1021/acssynbio.3c00292

Title: Automated Platform for the Plasmid Construction Process

Journal Article · 10 November 2023 · ACS Synthetic Biology

DOI: https://doi.org/10.1021/acssynbio.3c00292 · OSTI ID:2205410

Nava, Alberto A. ^[1]; Fear, Anna Lisa ^[2]; Lee, Namil ^[2]; Mellinger, Peter ^[2];

^[3];

^[3]; Tan, Stephen ^[3]; Kaplan, Nurgul ^[3]; Goyal, Garima ^[3]; Coates, R. Cameron ^[3]; Roberts, Jacob ^[1]; Johnson, Zahmiria ^[4]; Hu, Romina ^[4]; Wu, Bryan ^[4]; Ahn, Jared ^[4]; Kim, Woojoo E. ^[2]; Wan, Yao ^[2]; Yin, Kevin ^[1];

^[3]; Haushalter, Robert W. ^[2] more »

Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; University of California, Berkeley, CA (United States)
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; USDOE Agile BioFoundry, Emeryville, CA (United States)
University of California, Berkeley, CA (United States)
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division; University of California, Berkeley, CA (United States); Shenzhen Institutes for Advanced Technologies, Shenzhen (China); Technical University of Denmark, Lyngby (Denmark)

There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J₅ DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO); National Science Foundation (NSF)

Grant/Contract Number:: AC02-05CH11231; EE0008926

OSTI ID:: 2205410

Alternate ID(s):: OSTI ID: 2356801

Journal Information:: ACS Synthetic Biology, Vol. 12, Issue 12; ISSN 2161-5063

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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automation
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polyketide synthases

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