The efficient and seamless assembly of DNA fragments, commonly referred to as Golden Gate Assembly (1,2), has its origins in 1996, when for the first time it was shown that multiple inserts could be assembled into a vector backbone using only the sequential (3) or simultaneous (4) activities of a single Type IIS restriction enzyme and T4 DNA ligase. Golden Gate Assembly and its derivative methods exploit the ability of Type IIS restriction endonucleases (REases) to cleave DNA outside of the recognition sequence. The inserts and cloning vectors are designed to place the Type IIS recognition site distal to the cleavage site, such that the Type IIS REase can remove the recognition sequence from the assembly. The advantages of such an arrangement are three-fold:
- The overhang sequence created is not dictated by the REase, and therefore no scar sequence is introduced.
- The fragment-specific sequence of the overhangs allows orderly assembly of multiple fragments simultaneously.
- The restriction site is eliminated from the ligated product, so digestion and ligation can be carried out simultaneously.
The net result is the ordered and seamless assembly of DNA fragments in one reaction. The accuracy of the assembly is dependent on the length of the overhang sequences. Therefore, Type IIS REases that create 4-base overhangs (such as PaqCI®, BsaI-HF®v2, BbsI/BbsI-HF, BsmBI-v2 and Esp3I) are preferred. Insert assembly calls for careful design of overhangs to direct the assembly, as well as verification that the Type IIS REase sites used are not present in the fragments for the assembly of the expected product. The use of web tools such as the NEB Golden Gate Assembly Tool greatly simplifies both processes, making Golden Gate Assembly a robust technology that assembles single and multiple DNA fragments (5), even if repetitive elements are present (6) and can, if wished, introduce multiple site-directed mutations (7). Golden Gate Assembly has been widely used in the construction of custom-specific TALENs for in vivo gene editing (8), as well as in the cloning of inserts from diverse populations enabling library creation.
Recently, NEB has published research on T4 DNA Ligase Fidelity and multi-fragment assembly (9-11). This information, in conjunction with improved Type IIS restriction enzymes (e.g., BsaI-HFv2, NEB #R3733 and BsmBI-v2, NEB #R0739) and ligase fidelity tools, has enabled NEB to push the limits of Golden Gate Assembly. For more information, please visit www.neb.com/GoldenGate.
To help select the best DNA assembly method for your needs, please use our Synthetic Biology/DNA Assembly Selection Chart.
Visit Type IIS Restriction Enzymes for a comprehensive list of all Type IIS enzymes available from NEB and their characteristics.
- Engler, C., et al. (2008) PLoS ONE 3, e3647.
- Engler, C., et al. (2009) PLoS ONE 4, e5553.
- Lee, J.H., et al, (1996) Genet. Anal., e1647.
- Padgett, K.A. and Sorge, J.A. (1996) Gene, e7318.
- Werner, S., et al. (2012) Bioeng. Bugs, e18223.
- Scior, A., et al. (2011) BMC Biotechnol., e1187.
- Yan, P., et al. (2012) Anal. Biochem., e7029.
- Sanjana, N. E., et al. (2012) Nat. Protoc., e1431.
- Potapov, V. et. al. (2018) ACS Synth. Biol., e0333.
- Pryor, J. M. et al. (2020)PLoS One, e8592.
- Pryor, J.M., et al. (2022) ACS Synth. Biol. e0525.
Find out how Golden Gate Assembly can be used to quickly join multiple DNA fragments.
These days, restriction enzymes are being used in many more applications other than cloning. Learn more in this episode of NEB TV.
Advances in understanding ligase fidelity, bias, and efficiency in Golden Gate Assembly allows for assembly of more than 50 fragments in a single reaction.
Listen to DAD (Data-optimized Assembly Design) when constructing high-complexity Golden Gate Assembly targets
This webinar introduces insights and modified protocols for Golden Gate Assembly enabling 50+ DNA fragments to be faithfully assembled in a single reaction.
Type IIS restriction enzymes have both recognition and binding sites, but cut downstream of the recognition site, creating 4-base overhangs ideal for re-assembly. View a list of TypeIIS enzymes.
This video discusses Domestication, or the removal of Type IIS cut sites naturally occurring in vector or insert sequences, as it relates to Golden Gate Assembly.
This video demonstrates how to use the Golden Gate Assembly Tool, we will walk through selecting insert and plasmids, primer design to make amplicon inserts.