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Protocols

This page lists all the protocols used in our project. We have classified them into five main categories as follow.

General

Cell Transformation

- Remove competent cells from freezer and allow to thaw on ice for 10 mins

- Add 3-5μl of DNA to the cells

- Incubate on ice for 20 mins

- Heat shock the cells at 42°C for 45 seconds

- Add 500μl of LB Broth, and incubate in a shaker at 37°C for 1 hour

- Centrifuge for 10 minutes, remove and keep 100μl of the supernatant, and pour away the rest.

- Resuspend the pellet in the 100μl of supernatant that was removed earlier

- Spread 5μl onto one agar plate, and then pour the rest onto another. Incubate the plates overnight at 37°C.

DNA Rehydration

Colony PCR

- 20.75 ul H2O

- 2.5 ul Pfu Buffer

- 0.25 ul dNTP

- 0.5 ul forward primer

- 0.5 ul reverse primer

- 0.5 ul Pfu Cx polymerase

Make up a master mix of everything except polymerase and aliquot into PCR tubes. Pick colonies from your plate, spot onto your reference grid plate and then pipette up and down in the PCR tube. The high denaturation temperature of PCR lyses the cells so that the DNA contents can be used as template for sequencing primers to anneal to and polymerase to extend, so you can verify that the colonies contain your plasmid based on analytical gel electrophoresis.

CPEC assembly

Make up 50 ul reactions with 5 ul DNA total with each part to be assembled at equimolar concentrations (ie. make appropriate dilutions)

-33.5 ul ddH2O

-10 ul Phusion HF buffer (5x)

-1 ul dNTP mix (40 mM)

-5 ul DNA (1-50 ng)

-0.5 Phusion high fidelity DNA polymerase (2 U/ul^-1)

Extracting Fluorescent Protein Samples

- Colonies were picked from the plates containing the transformants, and these were grown in 5ml of LB Broth for 6 hours at 37°C. These starter cultures were then used to inoculate 100ml flasks of broth which were grown overnight on a shaker at 37°C.

- The cultures were transferred into 50ml Falcon tubes, and spun down in a centrifuge for 10 mins at 5000rpm. The supernatant was poured off, and the pellet resuspended in 20mM Tris Lysis buffer.

- The cell suspension was sonicated to lyse the cells, and then the samples were centrifuged again to collect cell debris. The supernatant was collected and stored in a refrigerator at 4°C. Do not freeze the samples, as this may cause protein degradation

Thermostability Assay

- Take 50ul of fluorescent protein sample and heat for 2 hours at the following temperatures (degrees centigrade) in a PCR thermocycler. 35.3, 37.1, 39.7, 44.1, 48.5, 52.5, 56.7, 57.1, 59.1, 61.3, 61.7, 65.7, 66.3, 69.7, 70.9, 72.5, 74.1, 75.3, 79.1, 83.7, 88.8, 92.3, 95.1, 96.5

- Dilute 30ul of heat treated samples in 170ul of lysis buffer and measure fluorescence on plate reader.

SOB/SOC

To make a litre of Super Optimal Broth (SOB):

20g peptone

5g yeast extract

0.58g NaCl

0.44g KCl

0.95g MgCl₂

1.2g MgSO₄

- Add the above ingredients to a flask, and then make up to a litre with distilled water

To make a litre of SOC, first make up a litre of SOB and then add:

3.6g Glucose

Glycerol stock preparation

- obtain the bacterial pellet from centrifugation
- resuspend the pellet with _microl dH20
- add _microl of 80% glycerol in each eppendorf.
- mix bacteria in 80% glycerol by pipetting up and down.
- freeze at -80° C.

@@ Line 65: / Line 65: @@
 <p>3.6g Glucose</p>
 <hr style="color:#225323;"/>
+<h2>Glycerol stock preparation</h2>
+<p>- obtain the bacterial pellet from centrifugation <br>
+- resuspend the pellet with _microl dH20 <br>
+- add _microl of 80% glycerol in each eppendorf.<br>
+- mix bacteria in 80% glycerol by pipetting up and down.<br>
+- freeze at -80° C. </p>
 </body>
 </html>

Team:Imperial College London/Protocols General