Golden Gate Assembly

Background and Design

Golden Gate cloning or Golden Gate assembly is a molecular cloning method that allows a researcher to simultaneously and directionally assemble multiple DNA fragments into a single piece using Type IIs restriction enzymes and T4/T7 DNA ligase. This assembly is performed in vitro. Most commonly used Type IIs enzymes include BsaI, BsmBI and BbsI. Unlike standard Type II restriction enzymes like EcoRI and BamHI, these enzymes cut DNA outside of their recognition sites and therefore can create non-palindromic overhangs. Since 256 potential overhang sequences are possible, multiple fragments of DNA can be assembled by using combinations of overhang sequences.


  • 10× T4 DNA ligase buffer (NEB: M0202S)
    • Why T4 DNA ligase buffer with T7 DNA ligase? T7 buffer contains PEG, which inhibits electroporation.
  • T7 DNA ligase (NEB: M0318S)
    • Why T7 DNA ligase instead of T4 DNA ligase? T7 does not ligate blunt ended DNA, yielding less off-target ligation.
  • Restriction endonuclease BsaI (NEB: R0535) or BsmBI (NEB: R0580S)
  • Competent cells
  • SOC and liquid media
  • Selective plates


Use the Calculator Spreadsheet (linked at the bottom of the page) for planning your reactions!

  1. Mix 20 fmol (1 nM final concentration) backbone and 40 fmol each insert of your DNA segments together. The volume of this mixture must be 16 無.
  2. Add water to a final volume of 16 痞
  3. Add 2 無 of 10× T4 DNA ligase buffer. Mix by vortexing.
  4. Add 1 無 of BsaI or BsmBI and 1 無 of T7 DNA ligase. Mix by gently pipetting.
  5. Incubate the reaction for 30 temperature cycles (42蚓 for 5 min and then 16蚓 for 5 min), followed by a final 10 min incubation at 55蚓.
  6. Use 2 無 of this assembly reaction for electroporation or 4 無 for transforming chemically competent cells.


  • Inserts should be screened for the presence of internal BsaI/BsmBI sites before they are used! You may need to edit these out.
  • The best option for Golden Gate assembly of modules involving inserts < 250 bp or > 3kb, or inserts containing repetitive elements that might accumulate errors during PCR amplification, is to clone these into the entry vector and use that for the assembly. For other modules, PCR amplicons can usually be used in place of parts cloned into the entry vector to save time.
  • A 2:1 insert:destination plasmid ratio is recommended, although the Golden Gate Assembly process is robust enough that 1:1 ratios also can be used. For PCR amplicons, the amount of each insert to be added can be calculated by molar calculations or relative length calculations.
  • Single insert cloning is more efficient than multiple insert cloning. Assembly efficiency decreases as the number of fragments increases. The presence of repetitive sequences in an insert will also decrease efficiency. For inserts < 250 bp or > 3 kbp, pre-cloning these inserts into the entry vector will increase efficiency.
  • The normal restrictions on overall plasmid size to allow transformation and stable maintenance in E. coli apply to Golden Gate assemblies. Efficiencies are highest when the product plasmid is < 12 kb. Larger assemblies can be made but may require larger numbers of colonies to be screened for the correct full length assembled products.
  • Cycling assemblies using 5-10 min temperature steps work well for larger scale assemblies (>10 inserts) and for any assembly for which maximal assembly yields and transformation levels are desired.


  1. Engler C, Kandzia R, Marillonnet S. (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3:e3647. Link
  2. Lee ME, DeLoache WC, Cervantes B, Dueber JE. (2015) A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth. Biol. 4:975986. Link
  3. "Golden Gate Assembly". New England Biolabs. Retrieved 8 June 2015. Link
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