Protocols

1. Gibson
Gibson assembly is an exonuclease-based method to assembly multiple DNA fragments in correct order (1). The method was invented in 2009 by Daniel G. Gibson, of the J. Craig Venter Institute. The assembly reaction is carried out in one single reaction-tube, all at once, at 50° Celsius for 15-60 minutes. The process involves three different enzymatic actions. A 5’ exonuclease creates overhangs, enabling matched fragments to anneal. Then a DNA polymerase fills gap between the annealed strands and the 5´ end. Finally, a DNA ligase seals the gaps between the filled in gap and the annealed strands.


Protocol used for Gibson

(i) Modifications
V_insert = x
V_vector = y
V_gibson = x+y
V_water = 0µl
(ii) Incubation for 1h, not 15 min (iii) Before transformation: One transformation with x ul concentrated Gibson solution and one transformation with Gibson solution diluted 1:3 and transformation with 3*x ul diluted Gibson solution.

2. Transformation

E.coli TOP10: One Shot® TOP10 E. coli are provided at a transformation efficiency of 1 x 109 cfu/µg supercoiled DNA and are ideal for high-efficiency cloning and plasmid propagation. They allow stable replication of high-copy number plasmids.
Chemical Transformation Procedure
Modifications
In Step 5, Incubate for exactly 30-45 seconds in the 42°C water bath. Do not mix or shake. In Step 7, Add 200-250 µl of rom temperatured S.O.C medium to each vial. S.O.C is a rich medium; sterile technique must be practiced to avoid contamination

E.coli DH5Alpha: Modifications: Step 15 and Step 16 not done

3. PCR
The goal of PCR is to amplify a section of DNA of interest for DNA analysis (e.g. gene insertion, sequencing, etc). The amplification rate is exponential.
• Tag polimerase (25µl reaction)
Protocol Here
• Phusion polymerase (20µl reaction?):
Protocol Here
4. Gel
For making a small 1% gel:
Weigh out 0.5 g of agarose and mix it with 50 ml of 1x TAE buffer in a 100 ml Erlenmeyer flask.
Dissolve the agarose by bringing the mixture to the boiling point in a microwave oven, followed by mixing (by swirling the flask). Repeat the heating and mixing until all the agarose has dissolved.
Cool the agarose solution to ~50 o C by leaving it on the bench for ~20 min (or you may accelerate the cooling by applying cold water from the tap to the outside of the flask).
Using gloves, add 5 l GelRed (10 000x). Swirl the flask gently to mix, try to avoid bubbles.
Pour the gel carefully into the mold. Bubbles may be removed/punctured by using a pipette tip.
5. Miniprep

Protocol Modifications:
During the first attempt ethanol was not added to the PE buffer, which resulted in an unsuccessful miniprepl
In the second attempt 72/4% ethanol was added, as opposed to the recommended 96-100%, resulting in a successful miniprep
6. INTERLAB
96-Well Transformation Protocol:
Protocol
Plate reader protocol: Protocol