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Team:Tsinghua/Notebook
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'''2. BioBrick Parts Making Protocol''' | '''2. BioBrick Parts Making Protocol''' | ||
| - | 1. get desired sequences through NCBI or other sources and check for restriction sites | + | 1. get desired sequences through NCBI or other sources and check for restriction sites |
For no (Xba1 or Spe1) | For no (Xba1 or Spe1) | ||
| - | + | GOTO STEP2 | |
| - | + | ELSE | |
| - | + | GOTO STEP9 | |
| - | 2. Design primers with half-prefix (Xba1) and half-suffix (Spe1) | + | 2. Design primers with half-prefix (Xba1) and half-suffix (Spe1) |
| - | 3. PCR from according genome/plasmid | + | 3. PCR from according genome/plasmid |
| - | 4. Purify PCR product using Gel Extraction Kit (Transgen) | + | 4. Purify PCR product using Gel Extraction Kit (Transgen) |
| - | 5. Digest with Xba1+Spe1 | + | 5. Digest with Xba1+Spe1 |
| - | 6. Ligation with pSB1AC3, which was digest with Xba1+Spe1 and treated with CIAP | + | 6. Ligation with pSB1AC3, which was digest with Xba1+Spe1 and treated with CIAP |
| - | 7. Transform to TOP10 cells | + | 7. Transform to TOP10 cells |
| - | 8. Identify clones with colony PCR | + | 8. Identify clones with colony PCR |
| - | + | GOTO STEP20 | |
| - | 9. Design primers with full-prefix and full-suffix | + | 9. Design primers with full-prefix and full-suffix |
10. PCR from according genome/plasmid | 10. PCR from according genome/plasmid | ||
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11. Purify PCR product using Gel Extraction Kit (Transgen) | 11. Purify PCR product using Gel Extraction Kit (Transgen) | ||
| - | + | FOR EcoR1 | |
| - | + | GOTO STEP12 | |
| - | + | ELSE | |
| - | + | GOTO STEP14 | |
12. Digest with Xba1+Pst1 | 12. Digest with Xba1+Pst1 | ||
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13. Ligation with pSB1AC3, which was digest with Xba1+Pst1 and treated with CIAP | 13. Ligation with pSB1AC3, which was digest with Xba1+Pst1 and treated with CIAP | ||
| - | + | GOTO STEP16 | |
14. Digest with EcoR1+Spe1 | 14. Digest with EcoR1+Spe1 | ||
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20. Extract plasmid and send sequencing | 20. Extract plasmid and send sequencing | ||
| - | End^^ | + | End^^ |
| - | + | ||
| - | + | ||
='''Wet-Lab Procedures'''= | ='''Wet-Lab Procedures'''= | ||
Revision as of 11:57, 29 October 2008
| HOME | Team | Project 1 | Project 2 | Parts | Modelling | Notebook | Doodle Board |
|---|
Basic Wet-lab protocols
1. PCR
| Reagent | Concentration/Activity | Volume (50uL System) | Volume (100uL System) |
| 10x Pyrobest buffer II | 10x | 5 | 10 |
| Pyrobest | 0.3 | 0.5 | |
| dNTPmix | 10mM each | 1 | 2 |
| Primer 1 | 10uM | 1 | 2 |
| Primer 2 | 10um | 1 | 2 |
| Template DNA | changeable | 0.5 | 1 |
| MgCl2(Deletable) | 0.2M | 0.5 | 1 |
| ddH2O | 40.5 | 81 |
(Pyrobest DNA polymerase from Takara Co.Ltd.)
| Step | Condition | Time |
| 1 | 95℃ | 5min |
| 2 | 95℃ | 30sec |
| 3 | [Tm(fu)-4]℃ | 30sec |
| 4 | 72℃ | DNA length/kb/min |
| 5 | RETURN TO STEP 2 | 30-35 cycles |
| 6 | 72℃ | 10min |
| 7 | 4℃ | HOLD |
2. Fusion PCR
The basic system is similar to common PCR. There are some notes to raise the fusion efficiency:
a. Complementary region length: 15-20bp
b. Raise the annealing temperature in the fusion step.
| Step | Condition | Time |
| 1 | 95℃ | 5min |
| 2 | 95℃ | 30-50sec |
| 3 | {Tm(fu)+[(-2)~5]}℃ | 40-80sec |
| 4 | 72℃ | DNA length/kb/min |
| 5 | RETURN TO STEP 2 | 10-15 cycles |
| 6 | 72℃ | 5min |
| 7 | Add amplification Primers | |
| 8 | 95℃ | 2-5min |
| 9 | 95℃ | 30sec |
| 10 | [Tm(fu)-4]℃ | 30sec |
| 11 | 72℃ | DNA length/kb/min |
| 12 | RETURN TO STEP 2 | 25-30 cycles |
| 13 | 72℃ | 10min |
| 14 | 4℃ | HOLD |
3. Restriction Digestion
| Reagent | Concentration/Activity | Volume(50uL system) |
| DNA | <1ug | |
| Restriction Enzyme buffer | 10x | 5uL |
| Enzyme 1 | 1uL | |
| Enzyme 2 | 1uL | |
| ddH2O | to 50uL |
Incubate at 37℃, 1.5 hrs or longer (Enzymes from Takara Co.Ltd or NEB).
4. Ligation
| Reagent | Volume(10uL system) |
| Solution I | 5uL |
| DNA fragment | 3.5uL(changeable) |
| Vector | 1.5uL(changeable) |
Incubate at 16-18℃,1hr or longer (Ligation Kit from Takara Co.Ltd).
5. Transformation
Wet-lab Notes
1. Advanced protocol for parts extraction
2. BioBrick Parts Making Protocol
1. get desired sequences through NCBI or other sources and check for restriction sites For no (Xba1 or Spe1)
GOTO STEP2
ELSE
GOTO STEP9
2. Design primers with half-prefix (Xba1) and half-suffix (Spe1)
3. PCR from according genome/plasmid
4. Purify PCR product using Gel Extraction Kit (Transgen)
5. Digest with Xba1+Spe1
6. Ligation with pSB1AC3, which was digest with Xba1+Spe1 and treated with CIAP
7. Transform to TOP10 cells
8. Identify clones with colony PCR
GOTO STEP20
9. Design primers with full-prefix and full-suffix
10. PCR from according genome/plasmid
11. Purify PCR product using Gel Extraction Kit (Transgen)
FOR EcoR1
GOTO STEP12
ELSE
GOTO STEP14
12. Digest with Xba1+Pst1
13. Ligation with pSB1AC3, which was digest with Xba1+Pst1 and treated with CIAP
GOTO STEP16
14. Digest with EcoR1+Spe1
15. Ligation with pSB1AC3, which was digest with EcoR1+Spe1 and treated with CIAP
16. Transform to TOP10 cells
17. Identify clones with colony PCR
18. Extract plasmid and site-directed mutate by fusion PCR
19. Transform to TOP10 cells
20. Extract plasmid and send sequencing
End^^
Wet-Lab Procedures
- Click on any day below to see what wet-lab procedures were conducted.
