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Title: PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction

Abstract

Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor- intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error- free construction of plasmids with virtually any sequences in a high-throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments within 3 days. PlasmidMaker should greatly expand the potential of synthetic biology.

Authors:
; ORCiD logo; ORCiD logo; ; ORCiD logo; ; ; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, IL (United States); CABBI
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1867945
Alternate Identifier(s):
OSTI ID: 1904381; OSTI ID: 1993847
Grant/Contract Number:  
SC0018420
Resource Type:
Published Article
Journal Name:
Nature Communications
Additional Journal Information:
Journal Name: Nature Communications Journal Volume: 13 Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; expression systems; genetic techniques; synthetic biology

Citation Formats

Enghiad, Behnam, Xue, Pu, Singh, Nilmani, Boob, Aashutosh Girish, Shi, Chengyou, Petrov, Vassily Andrew, Liu, Roy, Peri, Siddhartha Suryanarayana, Lane, Stephan Thomas, Gaither, Emily Danielle, and Zhao, Huimin. PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. United Kingdom: N. p., 2022. Web. doi:10.1038/s41467-022-30355-y.
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Enghiad, Behnam, Xue, Pu, Singh, Nilmani, Boob, Aashutosh Girish, Shi, Chengyou, Petrov, Vassily Andrew, Liu, Roy, Peri, Siddhartha Suryanarayana, Lane, Stephan Thomas, Gaither, Emily Danielle, & Zhao, Huimin. PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. United Kingdom. https://doi.org/10.1038/s41467-022-30355-y
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Enghiad, Behnam, Xue, Pu, Singh, Nilmani, Boob, Aashutosh Girish, Shi, Chengyou, Petrov, Vassily Andrew, Liu, Roy, Peri, Siddhartha Suryanarayana, Lane, Stephan Thomas, Gaither, Emily Danielle, and Zhao, Huimin. Mon . "PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction". United Kingdom. https://doi.org/10.1038/s41467-022-30355-y.
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@article{osti_1867945,
title = {PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction},
author = {Enghiad, Behnam and Xue, Pu and Singh, Nilmani and Boob, Aashutosh Girish and Shi, Chengyou and Petrov, Vassily Andrew and Liu, Roy and Peri, Siddhartha Suryanarayana and Lane, Stephan Thomas and Gaither, Emily Danielle and Zhao, Huimin},
abstractNote = {Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor- intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error- free construction of plasmids with virtually any sequences in a high-throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments within 3 days. PlasmidMaker should greatly expand the potential of synthetic biology.},
doi = {10.1038/s41467-022-30355-y},
journal = {Nature Communications},
number = 1,
volume = 13,
place = {United Kingdom},
year = {Mon May 16 00:00:00 EDT 2022},
month = {Mon May 16 00:00:00 EDT 2022}
}
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https://doi.org/10.1038/s41467-022-30355-y
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