Experiments
Making LB Medium
What we needed was 100mL of solid medium and 350mL of liquid medium. According to the formula, every 1L of medium requires 10g of tryptone, 5g of yeast extract, 10g of NaCl, and ddH2O. For the solid medium, a 1% concentration of agarose powder is needed for solidification.
After adding the ingredients together, we used a plastic sheet with filter paper in the middle to cover the flask and filter possible impurities during autoclaved sterilization. We sterilized for about 20 minutes and let the medium cool down. For the solid medium, we added 50µL of Kanamycin or Ampicillin antibiotic. And for the final step, we poured the melted solid medium into the Petri dishes on the clean bench.
Overview:
1. PCR
2. PCR Gel Electrophoresis
3. PCR Gel Purification
4. Double-enzyme digestion
5. T4 DNA ligase
6. DNA transformation to competent cells
1. PCR:
1) Use a pipette to add reagents in a PCR tube and mix up (which contains enzymes required for PCR; dNTPs; ddH2O; and Buffer). Next, add the primers into the tube. Afterward, divide the prepared mixture into 2 PCR tubes.
2) Put the PCR tube into the PCR machine. Close the lid and set the program.

Steps Temperature Time Number of cycles
Initial denaturation 94 ℃ 5 min
Denaturation 94 ℃ 30 sec 33
Primer annealing 55 ℃ 45 sec
Extension 72 ℃ 2 min
IFinal extension 72 ℃ 5 min
2. PCR Gel Electrophoresis
1) Since the DNA contains a negative electric charge, we placed the gel with wells toward the negative charge of the buffer tank, as the other side is positively charged. Keep in mind that the TAE buffer needs to fully cover the gel.
2) Added DNA loading buffer to the PCR product, according to its concentration.
3) After the electrophoresis, we put the gel under the ultra slim LED illuminator to see the DNA and cut out the gel with DNA fragments for the next step.
3. PCR Gel Purification
1) Cut down the gel containing the target fragment and calculate the weight difference in the EP tube from adding the gel by weighing the tube before and after adding the gel
2) Add 500µL B2 buffer to the gel, and water bath at 50℃ for 5-10 minutes to make the gel melt in the buffer
3) Move all the liquid into the absorption column with membrane, centrifuge for 30s, at 8000×g
4) Add 500µL Wash Solution, 9000×g centrifuge for 30s, repeat this step again
5) Centrifuge again for 2 minutes, 12000×g.
6) Put the absorption column into a clean 1.5mL centrifuge tube, add 30µL Elution Buffer, put it at room temperature for 2 minutes, and centrifuge for 1 minute to keep the DNA solution.
7) Measure the DNA concentration using the Nanodrop machine.
4. Double-enzyme digestion
1) add 2 μL each of the restriction enzyme into one micro-centrifuge tube.
2) add 5μL buffer, 10μL ddH₂O, and 1μL DNA into each micro-centrifuge tube.
3) 37℃ incubation for 1h.
4) Agarose Gel Electrophoresis and gel extraction.
5. T4 DNA ligase
1) add 1 μL T4 DNA ligase, 1 μL T4 DNA ligase buffer, 1 μL DNA fragment, 1 μL plasmid vector, and 5 μL ddH₂O into the microcentrifuge tube.
2) 22 ℃ water bath for 30 minutes.
6. DNA transformation to plasmid
1) Put the chemically competent cells DH5α on ice for 1-2 minutes.
2) Mix the DH5α competent cells with precooled recombinant plasmids. Ice bath for 30 minutes.
3) Heat shock at 42°C for 1 minute and put on ice immediately for 2 minutes.
4) Add 700μL LB medium and incubate it at 37℃, 200rpm for 60 minutes.
5) Centrifuge 8000rpm 1 min, get rid of 650µL of supernatant.
6) Resuspend the E. coli and coat it on the solid medium.
Overview:
1. Colony PCR
2. Plasmid Extraction
1. Colony PCR
ystem:
1. We added 5µL ddH₂O .
2. Added 10µL Primer S. Mixer (which includes dNTP, DNA polymerase, and reaction buffer).
3. Added 3µL of DNA template.
4. Added 1µL each of forward and reverse primer.
program:
1) 95℃, 5min, pre-degenerate
2) 95℃, 10s, DNA degeneration
3) 58℃, 30s, annealing
4) 72℃, elongation
5) 72℃, 10min, fully elongate
6) 4℃, infinite time, preserve
2. Plasmid Extraction
We cultured E. coli that to do plasmid extraction
1) Inoculate the bacteria and culture overnight, and centrifuge the cultured medium at 12000rpm for 1 min. Discard the supernatant
2) Add 500μl of the balance solution to the adsorption column, centrifuge the discard the filtrate
3) Add 250μl of Buffer SP1 from the Diamond Mini Plasmid Kit to the pellet cells. Add 250μl Buffer SP2 and 350μl Buffer SP3 and mix well.
4) Centrifuge at 12000rpm for 10 minutes, add the supernatant to the adsorption column, and centrifuge at 8000rpm for 30s.
5) Add 500 mL of wash solution, centrifuge at 9000×g for 30 seconds, and pour off the liquid in the tube (repeat once)
6) Centrifuge the empty adsorption column at 9000 ×g for 1 minute
7) Put the adsorption column into a new 1.5mL centrifuge tube, add 100 mL of Elution Buffer to the adsorption membrane, stand at room temperature for 1 minute, and centrifuge for 1 minute.
1) Inoculate the plasmid-containing strain in LB medium with corresponding antibiotics and culture overnight at 37℃, 200-220rpm.
2) Transfer the cultured medium into a 500mL LB culture medium, and add IPTG when the OD600 is around 0.6.
3) After overnight culturing, we verified the protein expression level by SDS-PAGE.
1) Inoculate the single colonies of the engineered strains in a triangular flask containing 10mL of fresh LB medium (containing antibiotics), and incubated at 37°C, 220 rpm for 12h.
2) 1 mL of bacterial cultured medium was added to a triangular flask containing 100mL of fresh LB medium (including 100mg/L Ampicillin) and incubated at 37°C, 220 rpm until the 0D600 was around 0.6.
3) The solution was divided into conical flasks, adding 50ml of cultured medium and L-tryptophan to a final concentration of 0.75mmol/L, 1mmol/L, 1.5mmol/L, 2mmol/L, 2.5mmol/L, and 3mmol / L and cultured at 22°C, 220 rpm for 7 hours. Samples were taken at 1h, 2h, 4h, 5h, 6h, 7h.
4) Fluorescence intensity was detected immediately by using 200 μL bacterial solution samples to a 96-well black microplate plate
1) We used the Glutamate Dehydrogenase (GDH) Activity Assay Kit to measure the protein activity.
2) The bacteria cells were collected by centrifugation into centrifugal tubes, treated samples in the proportion of bacteria: extract volume (mL) (500-1000): 1 (1 mL of 5 million bacteria), crushed by ice bath sonicated (power 20% or 200 W, ultrasonic for 3s, 10s interval, 30 repeats), centrifuged at 4℃ 8000 g for 10 min, and the supernatant was placed on ice for testing.
3) Absorption values at 340 nm were determined using a UV-visible spectrophotometer.