Programming biological operating systems: genome design, assembly and activation.
Abstract
The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
There is a general trend that the cost and efforts required rises exponentially with the increased size of the genome to be synthesized.
“There is a general trend that the cost and efforts required rises exponentially with the increased size of the genome to be synthesized”
From Large-Scale de Novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities (2021) · cites this paper as Gibson, 2014
Due to the low efficiency of in vitro assembly of long DNA fragments, in vivo assembly is the general choice in most previous studies.
“Due to the low efficiency of in vitro assembly of long DNA fragments, in vivo assembly is the general choice in most previous studies”
From Large-Scale de Novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities (2021) · cites this paper as Gibson, 2014
Cites
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 9,742 · see citing works
Self-citationZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013) · Trends in Biotechnology · doi:10.1016/j.tibtech.2013.04.004 · Cited by 3,820 · see citing works
Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis
Schwartz, D. C., & Cantor, C. R. (1984) · Cell · doi:10.1016/0092-8674(84)90301-5 · Cited by 2,859 · see citing works
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., et al. (2010) · Science · doi:10.1126/science.1190719 · Cited by 2,638 · see citing works
Self-citationThe Minimal Gene Complement of <i>Mycoplasma genitalium</i>
Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. (1995) · Science · doi:10.1126/science.270.5235.397 · Cited by 2,545 · see citing works
Programming cells by multiplex genome engineering and accelerated evolution
Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009) · Nature · doi:10.1038/nature08187 · Cited by 1,529 · see citing works
Initiation of translation in prokaryotes and eukaryotes
Kozak, M. (1999) · Gene · doi:10.1016/s0378-1119(99)00210-3 · Cited by 1,364 · see citing works
A Whole-Cell Computational Model Predicts Phenotype from Genotype
Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., Assad-Garcia, N., Glass, J. I., & Covert, M. W. (2012) · Cell · doi:10.1016/j.cell.2012.05.044 · Cited by 1,300 · see citing works
Complete Chemical Synthesis, Assembly, and Cloning of a <i>Mycoplasma genitalium</i> Genome
Gibson, D. G., Benders, G. A., Andrews-Pfannkoch, C., Denisova, E. A., Baden-Tillson, H., Zaveri, J., Stockwell, T. B., Brownley, A., Thomas, D. W., Algire, M. A., et al. (2008) · Science · doi:10.1126/science.1151721 · Cited by 1,243 · see citing works
Self-citationEnzymatic Assembly of Overlapping DNA Fragments
Gibson, D. G. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385120-8.00015-2 · Cited by 741 · see citing works
Self-citationSmith, H. O., Hutchison, C. A., Pfannkoch, C. M., & Venter, J. C. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2237126100 · Cited by 612 · see citing works
Ellis, H. M., Yu, D., DiTizio, T., & Court, D. L. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.121164898 · Cited by 564 · see citing works
Plasmid construction by homologous recombination in yeast
Ma, H., Kunes, S. M., Schatz, P. J., & Botstein, D. (1987) · Gene · doi:10.1016/0378-1119(87)90376-3 · Cited by 563 · see citing works
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., Tolonen, A. C., Gianoulis, T. A., Goodman, D. B., Reppas, N. B., et al. (2011) · Science · doi:10.1126/science.1205822 · Cited by 550 · see citing works
Genome Transplantation in Bacteria: Changing One Species to Another
Lartigue, C., Glass, J. I., Alperovich, N., Pieper, R., Parmar, P. P., Hutchison, C. A., Smith, H. O., & Venter, J. C. (2007) · Science · doi:10.1126/science.1144622 · Cited by 485 · see citing works
Gibson, D. G., Benders, G. A., Axelrod, K. C., Zaveri, J., Algire, M. A., Moodie, M., Montague, M. G., Venter, J. C., Smith, H. O., & Hutchison, C. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811011106 · Cited by 480 · see citing works
Self-citationSynthetic chromosome arms function in yeast and generate phenotypic diversity by design
Dymond, J. S., Richardson, S. M., Coombes, C. E., Babatz, T. D., Muller, H., Annaluru, N., Blake, W. J., Schwerzmann, J., Dai, J., Lindstrom, D. L., et al. (2011) · Nature · doi:10.1038/nature10403 · Cited by 476 · see citing works
Towards synthesis of a minimal cell
Forster, A. C., & Church, G. M. (2006) · Molecular Systems Biology · doi:10.1038/msb4100090 · Cited by 437 · see citing works
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca
Temme, K., Zhao, D., & Voigt, C. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120788109 · Cited by 421 · see citing works
Chan, L. Y., Kosuri, S., & Endy, D. (2005) · Molecular Systems Biology · doi:10.1038/msb4100025 · Cited by 359 · see citing works
Chemical synthesis of the mouse mitochondrial genome
Gibson, D. G., Smith, H. O., Hutchison, C. A., Venter, J. C., & Merryman, C. (2010) · Nature Methods · doi:10.1038/nmeth.1515 · Cited by 348 · see citing works
Self-citationCreating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast
Lartigue, C., Vashee, S., Algire, M. A., Chuang, R.-Y., Benders, G. A., Ma, L., Noskov, V. N., Denisova, E. A., Gibson, D. G., Assad-Garcia, N., et al. (2009) · Science · doi:10.1126/science.1173759 · Cited by 332 · see citing works
Self-citationDNA assembly for synthetic biology: from parts to pathways and beyond
Ellis, T., Adie, T., & Baldwin, G. S. (2011) · Integrative Biology · doi:10.1039/c0ib00070a · Cited by 307 · see citing works
Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides
Gibson, D. G. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp687 · Cited by 290 · see citing works
Self-citationKouprina, N., & Larionov, V. (2008) · Nature Protocols · doi:10.1038/nprot.2008.5 · Cited by 234 · see citing works
Computational tools for the synthetic design of biochemical pathways
Medema, M. H., van Raaphorst, R., Eriko Takano, A., & Rainer Breitling, A. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2717 · Cited by 227 · see citing works
Carr, P. A., & Church, G. M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1590 · Cited by 203 · see citing works
Synthetic Generation of Influenza Vaccine Viruses for Rapid Response to Pandemics
Dormitzer, P. R., Suphaphiphat, P., Gibson, D. G., Wentworth, D. E., Stockwell, T. B., Algire, M. A., Alperovich, N., Barro, M., Brown, D., Craig, S., et al. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3006368 · Cited by 196 · see citing works
Self-citationItaya, M., Tsuge, K., Koizumi, M., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503868102 · Cited by 191 · see citing works
The first half-century of nuclear transplantation
Gurdon, J. B., & Byrne, J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1337135100 · Cited by 189 · see citing works
Cloning whole bacterial genomes in yeast
Benders, G. A., Noskov, V. N., Denisova, E. A., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq119 · Cited by 175 · see citing works
Synthetic biology projects in vitroPreprint
Forster, A. C., & Church, G. M. (2006) · Genome Research · doi:10.1101/gr.5776007 · Cited by 163 · see citing works
Eukaryotic transcriptional control
Kornberg, R. D. (1999) · Trends in Genetics · doi:10.1016/s0168-9525(99)01901-0 · Cited by 147 · see citing works
Nuclear Transfer to Eggs and OocytesPreprint
Gurdon, J. B., & Wilmut, I. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a002659 · Cited by 144 · see citing works
Eukaryotic transcriptional control
Kornberg, R. D. (1999) · Trends in Cell Biology · doi:10.1016/s0962-8924(99)01679-7 · Cited by 136 · see citing works
Update on designing and building minimal cells
Jewett, M. C., & Forster, A. C. (2010) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.06.008 · Cited by 134 · see citing works
DNA synthesis, assembly and applications in synthetic biology
Ma, S., Tang, N. C., & Tian, J. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.05.001 · Cited by 113 · see citing works
Life at the speed of light: from the double helix to the dawn of digital life
Venter, J. C. (2014) · Choice Reviews Online · doi:10.5860/choice.51-3803 · Cited by 112 · see citing works
A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast
Jaschke, P. R., Lieberman, E., Rodriguez, J., et al. (2012) · Virology · doi:10.1016/j.virol.2012.09.020 · Cited by 110 · see citing works
Transfer of YACs up to 2.3 Mb intact into human cells with polyethylenimine
Marschall, P., Malik, N., & Larin, Z. (1999) · Gene Therapy · doi:10.1038/sj.gt.3300975 · Cited by 85 · see citing works
Direct transfer of whole genomes from bacteria to yeast
Karas, B. J., Jablanovic, J., Sun, L., Ma, L. M., Goldgof, G. M., Stam, J. A., Ramon, A., Manary, M. J., Winzeler, E. A., Venter, J. C., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2433 · Cited by 84 · see citing works
Self-citationRapid, modular and reliable construction of complex mammalian gene circuits
Guye, P., Li, Y., Wróblewska, L., Duportet, X., & Weiss, R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt605 · Cited by 83 · see citing works
Assembly of Large, High G+C Bacterial DNA Fragments in Yeast
Noskov, V. N., Karas, B. J., Young, L., Chuang, R.-Y., Gibson, D. G., Lin, Y.-C., Stam, J. A., Yonemoto, I. T., Suzuki, Y., Andrews-Pfannkoch, C. M., et al. (2012) · ACS Synthetic Biology · doi:10.1021/sb3000194 · Cited by 82 · see citing works
Self-citationSequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast
Tagwerker, C., Dupont, C. L., Karas, B. J., Ma, L. M., Chuang, R.-Y., Benders, G. A., Ramon, A., Novotny, M. A., Montague, M. G., Venepally, P., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks823 · Cited by 66 · see citing works
Self-citationAn exogenous chloroplast genome for complex sequence manipulation in algae
O’Neill, B. M., Mikkelson, K. L., Gutierrez, N. M., Cunningham, J. L., Wolff, K. L., Szyjka, S. J., Yohn, C. B., Redding, K., & Mendez, M. J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1008 · Cited by 63 · see citing works
An Origin-Deficient Yeast Artificial Chromosome Triggers a Cell Cycle Checkpoint
van Brabant, A. J., Buchanan, C. D., Charboneau, E., Fangman, W. L., & Brewer, B. J. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00216-7 · Cited by 54 · see citing works
Karas, B. J., Tagwerker, C., Yonemoto, I. T., Hutchison, C. A., & Smith, H. O. (2011) · ACS Synthetic Biology · doi:10.1021/sb200013j · Cited by 52 · see citing works
Gene and Genome Construction in Yeast
Gibson, D. G. (2011) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb0322s94 · Cited by 31 · see citing works
Self-citationOligonucleotide Assembly in Yeast to Produce Synthetic DNA Fragments
Gibson, D. G. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-564-0_2 · Cited by 24 · see citing works
Self-citationConstructing large DNA segments by iterative clone recombination
Smailus, D. E., Warren, R. M., & Holt, R. A. (2007) · Systems and Synthetic Biology · doi:10.1007/s11693-008-9011-6 · Cited by 9 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Large-scale de novo DNA synthesis: technologies and applications
Kosuri, S., & Church, G. M. (2014) · Nature Methods · doi:10.1038/nmeth.2918 · Cited by 869 · see citing works
Hao, Y., Li, Q., Fan, C., & Wang, F. (2021) · Small Structures · doi:10.1002/sstr.202000046 · Cited by 90 · see citing works
Song, L.-F., Deng, Z.-H., Gong, Z.-Y., Li, L.-L., & Li, B.-Z. (2021) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.689797 · Cited by 74 · see citing works
- Authors
- Gibson, D. G.
- Affiliations
- J. Craig Venter Institute (US)
- Corresponding author
- Gibson, Daniel G
- Venue
- Nature Methods
- Published
- 2014-04-29
- Volume
- 11
- Issue
- 5
- Pages
- 521-526
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1970045399
- Cited by
- 65
- References
- 50
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 5 · 2023: 2 · 2021: 6 · 2020: 6 · 2019: 4 · 2018: 5 · 2017: 10 · 2016: 9 · 2015: 9 · 2014: 4
- FWCI
- 4.37
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- synthetic biology, synthetic genome, bacterial genome assembly, genome activation, genome design, genome editing, artificial cells, genome synthesis
- MeSH terms
- Biotechnology, Cell-Free System, Cloning, Molecular, Deoxyribonucleases, DNA, Gene Expression Regulation, Genetic Engineering, Genetic Vectors, Mycoplasma, Saccharomyces cerevisiae, Genome, Bacterial, Systems Biology, Synthetic Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review