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Rapid genome recoding by iterative recombineering of synthetic DNA

Yu Heng Lau, Finn Stirling, James Kuo, Michiel A.P. Karrenbelt, Yujia A. Chan, Adam Riesselman, Connor A. Horton, Elena Schaefer, David Lips, Matthew T. Weinstock, Daniel G. Gibson, Jeffrey C. Way, Pamela A. Silver
doi: https://doi.org/10.1101/115493
Yu Heng Lau
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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Finn Stirling
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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James Kuo
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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Michiel A.P. Karrenbelt
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
cSystems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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Yujia A. Chan
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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Adam Riesselman
dProgram in Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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Connor A. Horton
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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Elena Schaefer
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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David Lips
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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Matthew T. Weinstock
eSynthetic Genomics, Inc., 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
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Daniel G. Gibson
eSynthetic Genomics, Inc., 11149 North Torrey Pines Road, La Jolla, CA 92037, USA
fSynthetic Biology and Bioenergy Group, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
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Jeffrey C. Way
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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Pamela A. Silver
aWyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 5th Floor, Boston, MA 02115, USA
bDepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Alpert 536, Boston, MA 02115, USA
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Abstract

Genome recoding will provide a deeper understanding of genetics and transform biotechnology. We bypass the reliance of previous genome recoding methods on site-specific enzymes and demonstrate a rapid recombineering based strategy for writing genomes by Stepwise Integration of Rolling Circle Amplified Segments (SIRCAS). We installed the largest number of codon substitutions in a single organism yet published, creating a strain of Salmonella typhimurium with 1557 leucine codon changes across 200 kb of the genome.

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Posted March 09, 2017.
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Rapid genome recoding by iterative recombineering of synthetic DNA
Yu Heng Lau, Finn Stirling, James Kuo, Michiel A.P. Karrenbelt, Yujia A. Chan, Adam Riesselman, Connor A. Horton, Elena Schaefer, David Lips, Matthew T. Weinstock, Daniel G. Gibson, Jeffrey C. Way, Pamela A. Silver
bioRxiv 115493; doi: https://doi.org/10.1101/115493
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Rapid genome recoding by iterative recombineering of synthetic DNA
Yu Heng Lau, Finn Stirling, James Kuo, Michiel A.P. Karrenbelt, Yujia A. Chan, Adam Riesselman, Connor A. Horton, Elena Schaefer, David Lips, Matthew T. Weinstock, Daniel G. Gibson, Jeffrey C. Way, Pamela A. Silver
bioRxiv 115493; doi: https://doi.org/10.1101/115493

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