- 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 BsaI/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 (9) . 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., Kandzia, R., and Marillonnet, S. (2008) PLoS ONE 3, e3647.
- Engler, C., et al. (2009) PLoS ONE 4, e5553.
- Lee, J.H. et al, (1996) Genetic Analysis: Biomolecular Engineering, 13: 139-145.
- Padgett, K.A. and Sorge, J.A. (1996) Gene, 168: 31-35.
- Werner, S., et al. (2012) Bioeng. Bugs 3, 38-43.
- Scior, A., et al. (2011) BMC Biotechnol. 11, 87.
- Yan, P., et al. (2012) Anal. Biochem. 430, 65-67.
- Sanjana, N. E., et al. (2012) Nat. Protoc. 7, 171-192.
- Potapov, V. et. al. “Comprehensive Profiling of Four Base Overhang Ligation Fidelity by T4 DNA Ligase and Application to DNA Assembly.” ACS Synth. Biol. . DOI: 10.1021/acssynbio.8b00333.
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.
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.