Automated Platform for the Plasmid Construction Process

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

doi:10.1021/acssynbio.3c00292

Automated Platform for the Plasmid Construction Process

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

^*Corresponding author for this work

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Abstract

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.

Original language	English
Journal	ACS Synthetic Biology
Volume	12
Issue number	12
Pages (from-to)	3506-3513
ISSN	2161-5063
DOIs	https://doi.org/10.1021/acssynbio.3c00292
Publication status	Published - 2023

Keywords

Synthetic biology
Automation
Plasmid construction
Polyketide synthases

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10.1021/acssynbio.3c00292Licence: CC BY

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Nava, A. A., Fear, A. L., Lee, N., Mellinger, P., Lan, G., McCauley, J., Tan, S., Kaplan, N., Goyal, G., Coates, R. C., Roberts, J., Johnson, Z., Hu, R., Wu, B., Ahn, J., Kim, W. E., Wan, Y., Yin, K., Hillson, N., ... Keasling, J. D. (2023). Automated Platform for the Plasmid Construction Process. ACS Synthetic Biology, 12(12), 3506-3513. https://doi.org/10.1021/acssynbio.3c00292

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title = "Automated Platform for the Plasmid Construction Process",

abstract = "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.",

keywords = "Synthetic biology, Automation, Plasmid construction, Polyketide synthases",

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

note = "Publisher Copyright: {\textcopyright} 2023 The Authors. Published by American Chemical Society.",

year = "2023",

doi = "10.1021/acssynbio.3c00292",

language = "English",

volume = "12",

pages = "3506--3513",

journal = "ACS Synthetic Biology",

issn = "2161-5063",

publisher = "American Chemical Society",

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Nava, AA, Fear, AL, Lee, N, Mellinger, P, Lan, G, McCauley, J, Tan, S, Kaplan, N, Goyal, G, Coates, RC, Roberts, J, Johnson, Z, Hu, R, Wu, B, Ahn, J, Kim, WE, Wan, Y, Yin, K, Hillson, N, Haushalter, RW & Keasling, JD 2023, 'Automated Platform for the Plasmid Construction Process', ACS Synthetic Biology, vol. 12, no. 12, pp. 3506-3513. https://doi.org/10.1021/acssynbio.3c00292

TY - JOUR

T1 - Automated Platform for the Plasmid Construction Process

AU - Nava, Alberto A.

AU - Fear, Anna Lisa

AU - Lee, Namil

AU - Mellinger, Peter

AU - Lan, Guangxu

AU - McCauley, Joshua

AU - Tan, Stephen

AU - Kaplan, Nurgul

AU - Goyal, Garima

AU - Coates, R. Cameron

AU - Roberts, Jacob

AU - Johnson, Zahmiria

AU - Hu, Romina

AU - Wu, Bryan

AU - Ahn, Jared

AU - Kim, Woojoo E.

AU - Wan, Yao

AU - Yin, Kevin

AU - Hillson, Nathan

AU - Haushalter, Robert W.

AU - Keasling, Jay D.

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - Synthetic biology

KW - Automation

KW - Plasmid construction

KW - Polyketide synthases

U2 - 10.1021/acssynbio.3c00292

DO - 10.1021/acssynbio.3c00292

M3 - Journal article

C2 - 37948662

AN - SCOPUS:85178163917

SN - 2161-5063

VL - 12

SP - 3506

EP - 3513

JO - ACS Synthetic Biology

JF - ACS Synthetic Biology

IS - 12

ER -

Automated Platform for the Plasmid Construction Process

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