Team:Berkeley/Project/Construction

We chose to use Golden Gate Assembly because it allowed us to either create single-pot libraries or the interchange of combinatorially expand the number of multi-gene devices with smaller constituent parts. Golden Gate Assembly is powered by type IIs restriction enzymes, which have many key features that should be mentioned:

1. They cut distal to their recognition sites. Because of this, we have full control over the resulting 4bp overhangs, giving us a theoretical choice between 4^4, or 256 different overhangs. In practice, we reduced this set, eliminating cases where at 2/4 bases matched and palindromes, to minimize chances of mis-annealing.
2. They not palindromic, and thus have directionality. Because the recognition site is non-palindromic, the cutting can either happen to 5' or 3' to the recognition site. This can be modulated by reversing the sequence.
3. They can cut themselves out. Depending on the direction of cutting, the site can be cut out of the desired fragment so that it does not undergo digestion after it has been ligated.
4. Some are compatible with DNA ligase buffer.

An example type IIs restriction enzyme, BsmBI. In this diagram, a GACC overhang is created.

In classic Golden Gate Assembly, these type IIs enzymes together with T4 DNA Ligase to glue together these overhangs. Starting with either a 1) PCR product or a 2) plasmid, the assembly can be done in two ways:
A) Sequentially with an interstitial gel purification step, or
B) In a single reaction that oscillates between digestions and ligations to move towards a correct product. Because type IIs endonucleases cut distal to their recognition site, once they form a connection with the correct neighbor, the .