Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs

Hernandez Hernandez, Diana; Ding, Lin; Murao, Ayako; Dahlin, Lukas R.; Li, Gabriella; Arnolds, Kathleen L.; Amezola, Melissa; Klein, Amit; Mitra, Aishwarya; Mecacci, Sonia; Linger, Jeffrey G.; Guarnieri, Michael T.; Suzuki, Yo

doi:10.1021/acssynbio.3c00183

Title: Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs

Journal Article · 15 August 2023 · ACS Synthetic Biology

DOI: https://doi.org/10.1021/acssynbio.3c00183 · OSTI ID:1995319

^[1]; Ding, Lin ^[1]; Murao, Ayako ^[1]; Dahlin, Lukas R. ^[2]; Li, Gabriella ^[2]; Arnolds, Kathleen L. ^[2]; Amezola, Melissa ^[1]; Klein, Amit ^[3]; Mitra, Aishwarya ^[3]; Mecacci, Sonia ^[1]; Linger, Jeffrey G. ^[2]; Guarnieri, Michael T. ^[2];

^[1]

Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, United States
National Renewable Energy Laboratory, Golden, Colorado 80401, United States
Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, United States, Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1995319

Journal Information:: ACS Synthetic Biology, Journal Name: ACS Synthetic Biology Journal Issue: 9 Vol. 12; ISSN 2161-5063

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (13)

A Three-Way Combinatorial CRISPR Screen for Analyzing Interactions among Druggable Targets Zhou, Peng; Chan, Becky K. C.; Wan, Yuk Kei Cell Reports, Vol. 32, Issue 6 https://doi.org/10.1016/j.celrep.2020.108020	journal	August 2020
Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network Celaj, Albi; Gebbia, Marinella; Musa, Louai Cell Systems, Vol. 10, Issue 1 https://doi.org/10.1016/j.cels.2019.09.009	journal	January 2020
Biotechnology for secure biocontainment designs in an emerging bioeconomy Arnolds, Kathleen L.; Dahlin, Lukas R.; Ding, Lin Current Opinion in Biotechnology, Vol. 71 https://doi.org/10.1016/j.copbio.2021.05.004	journal	October 2021
Massively parallel high-order combinatorial genetics in human cells Wong, Alan S. L.; Choi, Gigi C. G.; Cheng, Allen A. Nature Biotechnology, Vol. 33, Issue 9 https://doi.org/10.1038/nbt.3326	journal	September 2015
Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection Suzuki, Yo; Onge, Robert P. St; Mani, Ramamurthy Nature Methods, Vol. 8, Issue 2 https://doi.org/10.1038/nmeth.1550	journal	January 2011
Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA Cost, Gregory J. Nature Protocols, Vol. 2, Issue 9 https://doi.org/10.1038/nprot.2007.325	journal	September 2007
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample Caporaso, J. G.; Lauber, C. L.; Walters, W. A. Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1 https://doi.org/10.1073/pnas.1000080107	journal	June 2010
Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics Cheng, A. A.; Ding, H.; Lu, T. K. Proceedings of the National Academy of Sciences, Vol. 111, Issue 34 https://doi.org/10.1073/pnas.1400093111	journal	August 2014
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM Wong, Alan S. L.; Choi, Gigi C. G.; Cui, Cheryl H. Proceedings of the National Academy of Sciences, Vol. 113, Issue 9 https://doi.org/10.1073/pnas.1517883113	journal	February 2016
Design and synthesis of a minimal bacterial genome Hutchison, C. A.; Chuang, R. -Y.; Noskov, V. N. Science, Vol. 351, Issue 6280 https://doi.org/10.1126/science.aad6253	journal	March 2016
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes Engler, Carola; Gruetzner, Ramona; Kandzia, Romy PLoS ONE, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pone.0005553	journal	May 2009
Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies Kostylev, Maxim; Otwell, Anne E.; Richardson, Ruth E. PLOS ONE, Vol. 10, Issue 9 https://doi.org/10.1371/journal.pone.0137466	journal	September 2015
Rescue of Infectious Sindbis Virus by Yeast Spheroplast-Mammalian Cell Fusion Ding, Lin; Brown, David M.; Glass, John I. Viruses, Vol. 13, Issue 4 https://doi.org/10.3390/v13040603	journal	April 2021

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