01/23/2015
Sent out untreated Luc14 gDNA PCR product of P197/P198 for sequencing:
Label
|
Primer
|
Direction
|
RD-1-3 |
P175 |
F
|
RD-4-6 |
P161 |
F
|
RD-7-9 |
P173 |
F
|
RD-10-12 |
P159 |
F
|
RD-13-15 |
P170 |
R
|
RD-16-18 |
P156 |
R
|
RD-19-21 |
P172 |
R
|
RD-22-24 |
P158 |
R
|
Topo cloning and quantification of editing efficiency with restriction enzyme'
cutting 1μg of untreated and g033 and g034 treated Luc14 cells gDNA PCRd with P197/P198 and column purified samples from 14.12.06 experiment with PfoI at 37°C for 3 hours.
Sample Read#
|
ng/µL
|
ul for 1ug
|
ul H2O
|
ul buffer
|
ul PfoI
|
Untreated |
85.402 |
11.71 |
5.29 |
2 |
1
|
g033 |
78.942 |
12.67 |
4.33 |
2 |
1
|
g034 |
80.841 |
12.37 |
4.63 |
2 |
1
|
Quantification with 1% agarose gel
Topo cloning
- purify uncut band from agarose gel
- add 'A's to the ends of the uncut products
- From the manual:
- After purification, add Taq polymerase buffer, dATP, and 0.5 unit of Taq polymerase. Incubate the reaction for 10–15 minutes at 72°C and use in the TOPO® Cloning reaction.
- Set up the TOPO Cloning reaction
- Mix the reaction below gently and incubate for 5 minutes at room temperature (22°C to 23°C):
Reagent*
|
Volume
|
Fresh PCR product |
0.5–4 µL
|
Salt Solution |
1 µL
|
Water |
add to a total volume of 5 µL
|
TOPO® vector |
1 µL
|
Final Volume |
6 µL
|
- Notes from the manual:
- Note: The red or yellow color of the TOPO® vector solution is normal and is used to visualize the solution.
- A Salt Solution (1.2 M NaCl; 0.06 M MgCl2) is provided to adjust the TOPO® Cloning reaction to the recommended concentration of NaCl and MgCl2... We have found that including salt (200 mM NaCl, 10 mM MgCl2) in the TOPO® Cloning reaction can increase the number of transformants 2- to 3-fold. In addition, incubating the reaction mixture for greater than 5 minutes in the presence of salt can also increase the number of transformants... Including salt in the TOPO® Cloning reaction allows for longer incubation times because it prevents topoisomerase I from rebinding and potentially nicking the DNA after ligating the PCR product and dissociating from the DNA. The result is more intact molecules, leading to higher transformation efficiencies.
- For most applications, 5 minutes will yield sufficient colonies for analysis. Depending on your needs, the length of the TOPO®-cloning reaction can be varied from 30 seconds to 30 minutes. For routine subcloning of PCR products, 30 seconds may be sufficient. For large PCR products (greater than 1 kb) or if you are TOPO®-cloning a pool of PCR products, increasing the reaction time will yield more colonies.
- You may store the TOPO® Cloning reaction at −20°C overnight.
- Place the reaction on ice and proceed to Transform One Shot® competent cells
Note: It is essential that LB plates containing ampicillin are pre-warmed prior to
spreading.
1. Add 4 µL of the TOPO® Cloning reaction from Set up the TOPO® Cloning
reaction, step 2 on page 13, into a vial of One Shot® chemically competent
E coli and mix gently. Do not mix by pipetting up and down.
2. Incubate on ice for 5 minutes.
3. Spread 50 µL of cells on a prewarmed LB plate containing 50–100 µg/mL
ampicillin and incubate overnight at 37°C.
4. An efficient TOPO® Cloning reaction should produce several hundred
colonies. Pick ~10 colonies for analysis (see Analyze positive clones on
page 20).
|