Team:NYMU-Taipei/experimentsandresults
Cell Model
FRET Model
Protocols
E.coli Protocols
We used an efficient two day cloning cycle split into a "Light" day and a "Heavy" day.
Light Day
The light day consists of Colony PCR and liquid culture of colonies transformed from a previous day.
-
The 3-in-1
First, count the number of colonies you want to check. Then, do the following 3 things sequentially:
- Liquid culture
- 2nd time plate
- Colony PCR
(Use the same tip to add the template to these three things)
- Make The Gel For Electrophoresis
- Run Gel Electrophoresis To Check The Colony PCR Product
Heavy Day
The heavy day consists of:
- Previously grown plasmid extraction
- Plasmid PCR
- Gel extraction
- Digestion
- Ligation
- Transformation
- Make the Colony PCR mix (we use Thermo' DreamTaq) with the mix amount slightly modified:
Item uL Primer(Forward and reverse) 1 dNTP (10mM) 1 10x DreamTaq buffer 5 Taq Polymerase 0.2 ddH20 42.8 Total 50 - Select a colony using a tip or toothpick.
- Dip it in a PCR tube and swirl it around.
PCR run protocol
Temperature Time 94℃ 60s 94℃ 15s 55℃ 20s 30-35 cycles 72℃ 1kb/min + 5-10s 72℃ 300s
- Aliquot 4 mL of LB medium in a centrifugal tube for each colony.
- Use a tip and dip it in the LB culture and swirl it around.
Take out new plates from the fridge and divide them into smaller sections. This is the second-time plate. Make sure to write the date on it. Cross out in red pen any sections you know is wrong after the Colony PCR check.
- Make 200mL of gel at a time and select a relevant percentage (e.g. 1%, 1.5%, or 2%)
- Measure out the relevant percentage in agarose (e.g. 1g of agarose for 100mL of 1% gel).
- Fill it up with 1xTAE buffer.
- Microwave on low, constantly taking it out every so often to swirl and mix it. Keep microwaving until clear. Make sure it is completely clear
- Cool to a temperature that is still hot but still can be held in your hand. If the gel gets too cold and starts to harden, start microwaving again until clear.
- Add 5uL of Safe-seeing dye for every 100mL of gel after cooled to the correct tempearature. Mix it well by swirling
- Pour it onto the molds quickly. Put a cover on it to block out the light.
- Wait at least 15-20 min until using it.
- Store in 4°C and away from light.
- Select a relevant % agarose gel based on your own experience
- Load 5uL from each tube of Colony PCR, mix it with 1uL of 6x DNA Dye and put it in a well.
- Load 3uL of marker into a well.
- Run in the 13x13cm box at 60V or 70V and 400mA for the desired amount of time.
- View in the gel viewer machine.
| Item | uL |
|---|---|
| Primer(Forward and reverse) | 0.2 |
| Template(100ng) | ? |
| dNTP (10mM) | 0.2 |
| 10x DreamTaq buffer | 1 |
| Taq Polymerase | 0.04 |
| ddH20 | to 10 uL |
| Total | 10 |
| Item | uL |
|---|---|
| Primer(Forward and reverse) | 0.2 |
| Template(100ng) | ? |
| dNTP (10mM) | 0.2 |
| 10x KOD buffer | 1 |
| KOD Polymerase | 0.04 |
| Mg2+ | |
| ddH20 | to 10 uL |
| Total | 10 |
Insert and backbone:
| Item | |
|---|---|
| DNA | 600 or 1000ng |
| 10x Buffer | 2uL |
| Enzyme1 | 0.6 or 1 uL |
| Enzyme2 | 0.6 or 1 uL |
| ddH2O | to 20 uL |
| Total | 20 |
Backbone check:
To check if the backbone is cut.
| Item | |
|---|---|
| DNA | 100ng |
| 10x Buffer | 1 uL |
| Enzyme1 or 2 | 0.1 uL |
| ddH2O | to 10 uL |
| Total | 10 |
Digest for at least 1hr. Over 2hr is better. EcoRI doesn't have star activity when cut this way (even overnight)
We run insert digests and backbone digests with backbone check on a gel. Then use GeneAid's gel extraction kit. The modifications in the protocol include:
Warm EB to 60-70oC before elution.
Always use the Gel (sequencing) protocol for gel extraction.
We use Thermo's and NEB's T4 Ligase:
| Item | amount |
| Vector | 8.5uL, total of approximately 100ng of DNA. |
| Insert | |
| ddH2O | |
| 10x Ligase Buffer | 1 |
| T4 Ligase | 0.5 |
| Total | 10 |
Incubate at room temperature for 2hr then transform 1uL then put the remaining amount in a small bag and put in 4oC overnight in case the transformation fails and retransformation is required.
We majorly use commercial E. coli DH5α competent cells and BL21 competent cells we made by ourselves.
- Add 1uL of plasmid or ligation mix to 20 uL of competent cells.
- Put mixture on ice for 30 minutes.
- Heat shock at 42℃ for 1 min.
- Put the mixture back on ice for another 20 minutes.
- Add 200 uL of LB broth to repair the cell wall; incubate at 37oC for 1.5 hr.
- Plate it on a relevant antibiotic plate.
- Incubate plate at 37C overnight.