User:DrJones1935/22 July 2012
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(Created page with "====I. PCR==== *'''Mix Reagents:''' :*Mix according to the following table, where 2 = LacZ, 3 = CAT*, 4 = tet<sup>r</sup>, 0.1-0.3 = +template, and 0.4 = -template ::*For exampl...")
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(Created page with "====I. PCR==== *'''Mix Reagents:''' :*Mix according to the following table, where 2 = LacZ, 3 = CAT*, 4 = tet<sup>r</sup>, 0.1-0.3 = +template, and 0.4 = -template ::*For exampl...")
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Revision as of 23:23, 3 October 2012
I. PCR
- Mix Reagents:
- Mix according to the following table, where 2 = LacZ, 3 = CAT*, 4 = tetr, 0.1-0.3 = +template, and 0.4 = -template
- For example, 2.1 = lacZ sample, 2.4 = lacZ control
2.1 | 2.2 | 2.3 | 2.4 | 3.1 | 3.2 | 3.3 | 3.4 | 4.1 | 4.2 | 4.3 | 4.4 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Reagent | (uL) | (uL) | (uL) | (uL) | (uL) | (uL) | (uL) | (uL) | (uL) | (uL) | (uL) | (uL) |
water | 33.5 | 33.5 | 33.5 | 33.5 | 33.5 | 33.5 | 33.5 | 33.5 | 32.5 | 32.5 | 32.5 | 33.5 |
5x Phusion HiFi buffer | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 | 10 |
10 mM dNTP mix | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
10 uM primer (F) | 2.5 (p2f_2) | 2.5 (p2f_2 | 2.5 (p2f_2) | 2.5 (p2f_2) | 2.5 (p3f_2) | 2.5 (p3f_2) | 2.5 (p3f_2) | 2.5 (p3f_2) | 2.5 (p4f) | 2.5 (p4f) | 2.5 (p4f) | 2.5 (p4f) |
10 uM primer (R) | 2.5 (p2r_2) | 2.5 (p2r_2) | 2.5 (p2r_2) | 2.5 (p2r_2) | 2.5 (p3r) | 2.5 (p3r) | 2.5 (p3r) | 2.5 (p3r) | 2.5 (p4r_2) | 2.5 (p4r_2) | 2.5 (p4r_2) | 2.5 (p4r_2) |
Template | ECNR2 colony* | ECNR2 colony* | ECNR2 colony* | 0 | ECFI5 colony* | ECFI5 colony* | ECFI5 colony* | 0 | 1 (pBR322) | 1 (pBR322) | 1 (pBR322) | 0 |
Phusion HiFi polymerase | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 | 0.5 |
*For these templates, I touched a colony with a sterile pipette tip and spread it on the bottom of the PCR tube before adding reagents
- Run PCR
Step | Temp (oC) | Time |
---|---|---|
1 | 94 | 4 m |
2 | 94 | 30 s |
3 | 53 | 30 s |
4 | 72 | 1.5 m |
5 | GOTO 2 | 7x |
6 | 94 | 30 s |
7 | 66 | 30 s |
8 | 72 | 1.5 m |
9 | GOTO 6 | 30x |
10 | 72 | 5 m |
11 | 4 | ∞* |
- Store tubes on ice after PCR is finished
II. Agarose Gel Electrophoresis (AGE) of PCR Samples
- Make Gel:
- Measure out
0.5 g0.50238 g of agarose and add to a 250 mL E-flask - Add 50 mL of 0.5x TBE buffer and swirl to mix
- Cover flask with a Kimwipe and microwave for ~1 minute until clear
- Allow to cool to ~60 oC and pour into beaker for ethidium bromide (EtBr)
- Add 1 uL of EtBr stock to agarose and swirl to mix
- Immediately pour gel into tray with combs
- Allow to solidify, then remove the comb and tape and place the tray in the gel box with the wells closer to the black electrode
- Make sure it is submerged in TBE buffer
- Measure out
- Load Gel:
- Mix samples as drops on a piece of parafilm
- Mix:
Ladder (Invtrogen 1 kb plus) | Blank | Sample |
---|---|---|
*5 uL DNA ladder *1 uL 6x Loading Dye | *8.3 uL dH2O *1.7 uL 6x Loading Dye | *6.3 uL dH2O *1.7 uL 6x Loading Dye *2.0 uL DNA |
- Load ~10 uL (except ladder which is ~6 uL) on gel according to the following chart:
Lane 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NEB 2-log ladder | Blank | 2.1 | 2.2 | 2.3 | 2.4 | 3.1 | 3.2 | 3.3 | 3.4 | 4.1 | 4.2 | 4.3 | 4.4 | NEB 2-log ladder |
- Store DNA at 4 oC
- Run Gel:
- Close gel box and turn on power pack
- Run gel at 30 V for 20 min to stack gel
- Run gel at 75 V until the markers have reached near the bottom of the gel
- Image Gel:
- RESULTS:
Source: Media:Srk_2012-07-21_17hr_37min.tif
Feature | Expected Size (bp) |
---|---|
Leftover pBR322 | 4361 |
LacZ | 3151 |
CAT* | 729 |
tetr | 1265 |