A user’s guide to golden gate cloning methods and standards
Open accessAbstract
The continual demand for specialized molecular cloning techniques that suit a broad range of applications has driven the development of many different cloning strategies. One method that has gained significant traction is Golden Gate assembly, which achieves hierarchical assembly of DNA parts by utilizing Type IIS restriction enzymes to produce user-specified sticky ends on cut DNA fragments. This technique has been modularized and standardized, and includes different subfamilies of methods, the most widely adopted of which are the MoClo and Golden Braid standards. Moreover, specialized toolboxes tailored to specific applications or organisms are also available. Still, the quantity and range of assembly methods can constitute a barrier to adoption for new users, and even experienced scientists might find it difficult to discern which tools are best suited toward their goals. In this review, we provide a beginner-friendly guide to Golden Gate assembly, compare the different available standards, and detail the specific features and quirks of commonly used toolboxes. We also provide an update on the state-of-the-art in Golden Gate technology, discussing recent advances and challenges to inform existing users and promote standard practices.
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The shuttle vectors used by the authors include BsaI restriction sites that are compatible with modular Golden Gate cloning.
“the shuttle vectors used by the authors include BsaI restriction sites that are compatible with modular Golden Gate cloning.4”
From Protocol for the transformation and engineering of edible algae Arthrospira platensis to generate heterologous protein-expressing strains (2023) · cites this paper as [4]
The Hierarchical Assembly section says that GoldenBraid part vectors contain BsaI recognition sites, supporting the general compatibility of BsaI sites with modular Golden Gate cloning. The paper does not identify or describe the specific shuttle vectors used by the citing authors, so it cannot establish that those vectors contain BsaI sites. (LLM, conf=0.84)
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Strategies for the Development of Industrial Fungal Producing Strains
Salazar-Cerezo, S., de Vries, R. D., & Garrigues, S. (2023) · Journal of Fungi · doi:10.3390/jof9080834 · Cited by 57 · see citing works
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A Multiplex MoClo Toolkit for Extensive and Flexible Engineering of Saccharomyces cerevisiae
Shaw, W. M., Khalil, A. S., & Ellis, T. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.3c00423 · Cited by 49 · see citing works
A versatile microbial platform as a tunable whole-cell chemical sensor
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Modulating Microbial Materials - Engineering Bacterial Cellulose with Synthetic Biology
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High‐Complexity One‐Pot Golden Gate Assembly
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Navigating the challenges of engineering composite specialized metabolite pathways in plants
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SubtiToolKit: a bioengineering kit for Bacillus subtilis and Gram-positive bacteria
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Genetic engineering in diatoms: advances and prospects
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Ju, Y., Zhang, H., Du, X., Wei, J., Liu, J., Wei, L., Liu, Q., & Xu, N. (2023) · Metabolic Engineering · doi:10.1016/j.ymben.2023.08.002 · Cited by 17 · see citing works
CUBIC: A Versatile Cumate-Based Inducible CRISPRi System in Streptomyces
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Liu, H., Xiang, Y., Xiong, M., Xiao, X., Zhou, J., Tian, H., Chen, Q., & Li, Y. (2024) · Communications Biology · doi:10.1038/s42003-024-06398-w · Cited by 14 · see citing works
Standardizing cassette-based deep mutagenesis by Golden Gate assembly
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Design and construction towards a pan-microbial toolkitPreprint
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Automatic design of gene regulatory mechanisms for spatial pattern formation
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High-throughput yeast engineering in biofoundries: towards autonomous and scalable synthetic biology
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Villa, C. A., Marienhagen, J., Noack, S., & Wahl, A. (2023) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2023.102967 · Cited by 9 · see citing works
Tabakh, H., Jester, B. W., Zhao, H., Kuestner, R., Khuong, N., Shanitta, C., Takeuchi, R., & Roberts, J. (2023) · STAR Protocols · doi:10.1016/j.xpro.2023.102087 · Cited by 8 · see citing works
“Note: To simplify high throughput plasmid generation, the shuttle vectors used by the authors include BsaI restriction sites that are compatible with modular Golden Gate cloning.(4) Maps of backbone plasmids used by the authors are indicated in Figure 1.”
MethodJansen, Z., Alameri, A., Wei, Q., Kulhanek, D. L., Gilmour, A. R., Halper, S. M., Schwalm, N. D., & Thyer, R. T. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.00340-24 · Cited by 8 · see citing works
Sun, Y., Chen, J., & Pommier, Y. G. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad735 · Cited by 8 · see citing works
Zhang, C., Li, R., Baude, L., Reinhardt, D., Xie, Z., & Staehelin, C. (2024) · Biology · doi:10.3390/biology13010053 · Cited by 7 · see citing works
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Kaleidoscope megamolecules synthesis and application using self-assembly technology
Zhou, S., & Wei, Y. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108147 · Cited by 7 · see citing works
Dual-mode CRISPRa/i for genome-scale metabolic rewiring in Escherichia coli
Moon, S. Y., Kim, M. R., An, N., Noh, M. H., & Lee, J. Y. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf818 · Cited by 6 · see citing works
Advancements in Golden Gate Cloning: A Comprehensive Review
Laborda-Mansilla, J., & Garcia‐Ruiz, E. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4220-7_27 · Cited by 6 · see citing works
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Hong, W., Ha, S. G., Kwon, H. C., & Lee, S. (2025) · Molecules and Cells · doi:10.1016/j.mocell.2025.100234 · Cited by 5 · see citing works
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Structural determinants of SlpA-mediated phage recognition in Clostridioides difficile
Royer, A. L. M., Dion, É., Umansky, A. A., Avino, M., Soutourina, O. A., & Fortier, L. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013724 · Cited by 5 · see citing works
BOTany methods: accessible automation for plant synthetic biology
Qiande, M., Lin, A., Larson, L., & Voiniciuc, C. (2026) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiag066 · Cited by 5 · see citing works
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CRAPS: Chromosomal-Repair-Assisted Pathway Shuffling in Yeast
Dykstra, C. B., Pyne, M. E., & Martin, V. J. J. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.3c00170 · Cited by 4 · see citing works
Golden EGG, a simplified Golden Gate cloning system to assemble multiple fragments
Biró, J. B., Kecskés, K., Szegletes, Z., Güngör, B., Wang, T., Kaló, P., & Kereszt, A. (2024) · Scientific Reports · doi:10.1038/s41598-024-77327-4 · Cited by 4 · see citing works
Bacterial DNA methylases as novel molecular and synthetic biology tools: recent developments
Flores-Fernández, C. N., & O’Callaghan, C. A. (2025) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-025-13442-0 · Cited by 4 · see citing works
Rainbow screening: Chromoproteins enable visualized molecular cloning
Ba, F., Zhang, Y., Liu, W., & Li, J. (2024) · Biotechnology Journal · doi:10.1002/biot.202400114 · Cited by 4 · see citing works
Automation and Miniaturization of Golden Gate DNA Assembly Reactions Using Acoustic Dispensers
Köbel, T. S., & Schindler, D. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4220-7_9 · Cited by 4 · see citing works
Milburn, G., Morris, C. M., Kosola, E., Patel‐Tupper, D., Liu, J., Pham, D. H., Acosta‐Gamboa, L., Stone, W. D., Pardi, S. A., Hillman, K., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.12.632622 · Cited by 3 · see citing works
Venero, O. M., Ndeh, R., Pan, A., Patrikainen, P., Eriksson, M., Akhgari, A., Kakko, L., Nedorezova, D., Mohamed, O., Thomson, L., et al. (2026) · BMC Biotechnology · doi:10.1186/s12896-025-01098-7 · Cited by 3 · see citing works
Engineering scutellarin biosynthesis in Artemisia annua
Li, D., Wu, X., Qi, X., Zhang, Z., Zeng, L., Liu, X., Zhang, F., Lan, X., Chen, M., Nagdy, M. M., et al. (2025) · Plant Cell Reports · doi:10.1007/s00299-025-03471-4 · Cited by 3 · see citing works
DASH : a versatile and high‐capacity gene stacking system for plant synthetic biology
Zhao, C., Stepanova, A. N., & Alonso, J. M. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70179 · Cited by 3 · see citing works
Illuminating Glucomannan Synthases To Explore Cell Wall Synthesis Bottlenecks
Grieß-Osowski, A., Robert, M., Qiande, M., Clauss, S., & Voiniciuc, C. (2025) · ACS Synthetic Biology · doi:10.1021/acssynbio.5c00181 · Cited by 3 · see citing works
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A comparative review of DNA assembly strategies: From traditional to modern
Ta, H. K. K., Dang, L. M., & Nguyen, L. T. T. (2025) · Gene Reports · doi:10.1016/j.genrep.2025.102376 · Cited by 3 · see citing works
Engineering Rapamycin-Induced Dimerization for Control of Gene Expression in Plants
Schirmer, D., Reed, A. C., Pfotenhauer, A. C., & Lenaghan, S. C. (2026) · ACS Synthetic Biology · doi:10.1021/acssynbio.6c00125 · Cited by 3 · see citing works
De Novo Engineered Living Materials via Elastin-Like Polypeptide-Mediated Self-Assembly
Browning, S., Prati, D., Mascia, L., Magni, P., Pasotti, L., & Molinari, S. (2026) · ACS Synthetic Biology · doi:10.1021/acssynbio.6c00073 · Cited by 3 · see citing works
Modular DNA Construct Design for High-Throughput Golden Gate Assembly
Végh, P., Chapman, E., Gilmour, C., & Fragkoudis, R. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4220-7_4 · Cited by 3 · see citing works
Standardized Golden Gate Assembly Metadata Representation Using SBOL
Vidal, G., Vitalis, C., & Guillén, J. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4220-7_6 · Cited by 3 · see citing works
Crafting Genetic Diversity: Unlocking the Potential of Protein Evolution
Gali, V. K., Tee, K. L., & Wong, T. S. (2024) · SynBio · doi:10.3390/synbio2020009 · Cited by 2 · see citing works
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Kemp, P., Belmonte, M. B., Schmidt, M., Eisenhauer, K., Gebhardt, C., Kabuth, K., Koeppl, H., & Stein, V. (2026) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2026.03.008 · Cited by 2 · see citing works
Yeoh, J. X., Choong, Y. S., & Lim, T. S. (2025) · Protein Expression and Purification · doi:10.1016/j.pep.2025.106857 · Cited by 2 · see citing works
Galez, H., Brancotte, B., Bonche, J., Fumey, J., Napolitano, S., & Grégory Batt, A. (2025) · ACS Synthetic Biology · doi:10.1021/acssynbio.5c00553 · Cited by 2 · see citing works
Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT-2 and Flex
Malcı, K., Meng, F., Galez, H., Silva, A. F. D., Caro‐Astorga, J., Grégory Batt, A., & Ellis, T. (2026) · ACS Synthetic Biology · doi:10.1021/acssynbio.5c00629 · Cited by 2 · see citing works
Song, Y., Zeng, Z., Pan, L., Liao, A., Liu, N., Huang, J., Tian, H., & Wang, X. E. (2026) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2026.05.011 · Cited by 2 · see citing works
Metabolic engineering strategies for optimized lignan production in plants
Choi, S., Lee, S. B., & Kim, B. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1827862 · Cited by 2 · see citing works
A systematic screening assay identifies efficient small guide RNAs for CRISPR activation
Arvidsson, E., Lobo, D. D., Sabarese, E., Duarte, F. T., Nobre, R. J., Lundberg, C., & Quintino, L. (2025) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2025.1336313 · Cited by 2 · see citing works
Seamless, modular binary vectors for plant cell and molecular biology
Greenhalgh, R., Horner, W., Klimpel, K. A., Chatterjee, S., Scarpin, M. R., & Brunkard, J. O. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.70233 · Cited by 2 · see citing works
CloneCoordinate: Open-Source Software for Collaborative DNA Construction
Jeon, E., Shen, Z., Christ, S., Qi, E., Fan, I., Lee, N., Morgan, O., Ohl, M., Millson, D., Laker, M., et al. (2025) · ACS Synthetic Biology · doi:10.1021/acssynbio.5c00582 · Cited by 2 · see citing works
pGG-PIP: A GreenGate (GG) entry vector collection with Plant Immune system Promoters (PIP)Preprint
Calabria, J., Rast-Somssich, M. I., Wang, L., Chen, H.-W., Watt, M., Idnurm, A., Persson, S., & Somssich, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.20.521163 · Cited by 2 · see citing works
Benchmarking cassette-based deep mutagenesis by Golden Gate assemblyPreprint
Daffern, N., Francino-Urdaniz, I., Baumer, Z., & Whitehead, T. (2023) · bioRxiv · doi:10.1101/2023.04.13.536781 · Cited by 1 · see citing works
Aspergillus spp. As an Expression System for Industrial Biocatalysis and Kinetic Resolution
Garcia, P. H. D., Montico, J. R., Barichello, A. P., Pilissão, C., Contesini, F. J., Mortensen, U., & Carvalho, P. D. O. (2025) · Catalysts · doi:10.3390/catal15121174 · Cited by 2 · see citing works
ImPaqT, a Golden Gate-based immunological toolkit for zebrafish transgenesis
Hurst, S., Dimmler, C., & Cronan, M. R. (2026) · eLife · doi:10.7554/elife.104182.3 · Cited by 1 · see citing works
Selection of Fusion-Site Overhang Sets for High-Fidelity and High-Complexity Golden Gate Assembly
Lohman, G. J. S. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4220-7_3 · Cited by 1 · see citing works
Valenzuela, G. E. M., Gaibor, L., Castillo, T., & Espinoza, D. (2025) · Revista de investigación Agropecuaria Science and Biotechnology · doi:10.25127/riagrop.20251.1035 · Cited by 1 · see citing works
UniClo: scarless hierarchical DNA assembly without sequence constraint
Flores-Fernández, C. N., Lin, D., Robins, K. J., & O’Callaghan, C. A. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf548 · Cited by 1 · see citing works
Jurić, V., Erwin, L. G., O’Riordan, N. M., Maher, E., Holmes, J. D., & Young, P. W. (2026) · ACS Synthetic Biology · doi:10.1021/acssynbio.6c00085 · Cited by 1 · see citing works
Nandan, A., & Datta, S. (2026) · Springer eBooks · doi:10.1007/978-981-95-5378-5_1 · Cited by 1 · see citing works
Directed Evolution of an Efficient Polycarbonate Depolymerase With Exceptional Operational Stability
Jones, H. A., Hutton, A. E., Harris-Jukes, D., Davidson, J., Johannissen, L. O., Levy, C., Shaver, M. P., & Green, A. P. (2026) · Angewandte Chemie International Edition · doi:10.1002/anie.202525215 · Cited by 1 · see citing works
Trujillo‐Esquivel, E., Lorenzo-Manzanarez, J. L., Espinal‐Centeno, A., Méndez-Álvarez, D., Aguilar‐Cruz, A., Brieba, L. G., & Cruz‐Ramírez, A. (2026) · The Plant Cell · doi:10.1093/plcell/koag089 · Cited by 1 · see citing works
Protecting cells at the genetic level and simulating unauthorized access via a biohackathon
Kim, D., Kumar, I., Hassan, M. I., Barraza‐Vergara, L. F., Voigt, C. A., & Wilson, C. J. (2026) · Science Advances · doi:10.1126/sciadv.aeb8556 · Cited by 1 · see citing works
Rethinking the loop: toward integrated strain and bioprocess development
Stoltmann, T., & Noack, S. (2026) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2026.103493 · Cited by 1 · see citing works
Jiang, J., Dai, J.-L., Chen, H., Jiang, J., & Zhao, Q.-Z. (2026) · Bioresource Technology · doi:10.1016/j.biortech.2026.135370 · Cited by 1 · see citing works
Bülbül, E. F., Bang, S., George, K., Bianchi, G., Raj, P., Chung, S., Pauline, V., Hochstrasser, R., Minas, H. A., Elgaher, W. A. M., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-77963-6 · Cited by 1 · see citing works
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Generation of a plasmid series for rapid sub-cloning and use in various Enterobacteriaceae
Braun, H., Kanwal, N., Lopez, L. F. R., & Thomassin, J. (2024) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2024.08.006 · Cited by 1 · see citing works
Optogenetic Control of B. subtilis Gene Expression Using the CcaSR System
Haller, D. J., Castillo-Hair, S. M., & Tabor, J. J. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4047-0_1 · Cited by 1 · see citing works
Concise Overview of Methodologies Employed in the Study of Bacterial DNA Replication
Maciąg-Dorszyńska, M., Morcinek-Orłowska, J., & Barańska, S. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26020446 · Cited by 1 · see citing works
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One-pot cloning and protein expression platform for genetic engineeringPreprint
Sato, W., Sharon, J., Cash, B., Deich, C., Gaut, N. J., Heili, J. M., Engelhart, A. E., & Adamala, K. P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.28.672974 · Cited by 1 · see citing works
Bülbül, E. F., Bang, S., George, K., Bianchi, G., Raj, P., Chung, S., Pauline, V., Hochstrasser, R., Minas, H. A., Elgaher, W. A. M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.03.709401 · Cited by 2 · see citing works
- Authors
- Bird, J. E., Marles-Wright, J., & Giachino, A.
- Affiliations
- Newcastle University (GB)
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
- University of Salford (GB)
- Venue
- ACS Synthetic Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2022-11-02
- Volume
- 11
- Issue
- 11
- Pages
- 3551-3563
- ISSN
- 2161-5063 (ISSN-L)
- PMC
- PMC9680027
- OpenAlex
- W4307925826
- Cited by
- 135
- References
- 88
- Citations by year
- 2026: 40 · 2025: 43 · 2024: 32 · 2023: 19 · 2022: 1
- FWCI
- 2.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- ACS Synthetic Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of Salford Institutional Repository (University of Salford) (submittedVersion, cc-by)
- Newcastle University ePrints (Newcastle Univesity) (cc-by)
- Funders
- Ministry of Defence
- Research Councils UK (BB/N005570/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- Golden Gate assembly, type IIS restriction enzymes, modular cloning, sticky ends
- MeSH terms
- Cloning, Molecular, DNA, DNA Restriction Enzymes, Genetic Vectors, 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 ›
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