Team:Newcastle/Labwork/28 August 2009

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Stochastic Switch team

Summary

Today the pSB1AT3 DNA fragment cut from the gel yesterday was purified using the gel fragment cleaning kit, and as well as this a PCR was carried out with both the ara primers on Bacillus genomic DNA, and the sspb primers on E.coli genomic DNA prepared yesterday. We expected to see a ~170bp band for the ara regulatory sequence, and a ~570bp band for the sspb coding sequence.

We also continued to extract the plasmid backbone, pSB1AT3, cut with EcoRI and SpeI sites from the gel.

PCR

PCR was carried out with both the ara primers on Bacillus genomic DNA, and the sspb primers on E.coli genomic DNA prepared yesterday. We expected to see a ~170bp band for the ara regulatory sequence, and a ~570bp band for the sspb coding sequence. The Metal team were also doing PCR work today so we made our solutions as a whole to save time and resources. Overall there were 10 reactions.

We did our two PCRs as well as negative controls that contained everything other than the genomic DNA.

• Firstly the primers had to be rehydrated and put into Phil's primer database. The primers are rehydrated in PCR water. the volume of this is 5X the 'Amount Of Oligo' (nM) which can be found on the IDT datasheet for every oligo sent to us.

• To put them into the primer database, the name must be entered, as well as the sequence, number of bp and company used. (Ask Chris to log onto the database.) The primer number can be written on the blue cap.

• After rehydration 10ul of primer can be aliquoted into separate eppendorfs from the original tube sent. This means that the original tube probably won't have to be reopened again, and can be put into storage in the primer box in the -20 freezer. The 10ul aliquots can then be diluted again to 1:10, by adding 90ul PCR water. After use the primer aliquots can be put into a separate box in the -20 also (iGEM Diluted primers 1:10).

• As there were 10 reactions overall we made up 180ul of buffer mix (sufficient for 10 reactions +2 as the protocol suggests)

Added:

• • 60ul dNTPs
  • 60ul buffer
  • 60ul DMSO

These can be found in the 'stock solutions' box in the -20 freezer.

• We then diluted the taq Polymerase sufficient for our 10 reactions at 1 Unit per reaction. The taq stock is 5U/ul, therefore we used 3ul (enough for 15 reactions)of stock solution and 12ul PCR water.

• We entered all of our volumes of our solutions on a PCR Experiment sheet. The volume of water can be calculated by making the final volume up to 50ul.

• We labelled 4 PCR eppendorfs and added this appropriate amount of PCR water.
• Next 15ul of buffer mix was added.
• Next the primers were added- take care and keep reading the labels!
• Next the template DNA was added to the 2 tubes that are NOT controls.
• 1ul of the taq polymerase solution was added- to avoid mistakes this can be added to the master buffer solution instead.

The final solutions can be put into the PCR machine and the appropriate program set.

The PCR products can then be run on a gel which we did in the afternoon.

DNA Extraction

We took the eppendorf tube containing 184mg of gel from the fridge and solved the gel in 552ul(184*3) of gel solubilization solution. We left the tube containing the mix in 55C hot water bath for 10 minutes and vortexed every three minutes. We used two collection tubes and added 184 ul of isopropanol, 700ul of wash solution and 50ul of elute for each tube at the relevant steps. The first collection tube had 700ul of the solved gel whereas the second one had 450ul. 110ul of Elute was placed in an eppendorf tube and preheated in 65C prior to use. After adding the elute we left the tubes on the bench for a minute to incubate before the centrifuge. We got 100ul of DNA from the first tube and 80ul of from the second tube. We then combined the tubes, measured the DNA concentration and placed the tube to -20C fridge where midipreps are stored.

DNA Concentration

Concentration of the DNA was measured as 12ng/ul using the spectrophotometer

Promoter Library Sub-Project

So far, the work involved in this sub-project has seen pGFP-rrnB plasmid DNA digested with restriction enzymes EcoRI and NheI. The resulting 8kb DNA fragment was then extracted by firstly running the digested DNA through agarose gel in electrophoresis and then by excising the heavies band formed. The fragment DNA was then extracted from this removed piece of agarose by gel extraction kit and the 50ul of resulting DNA was stored in the -20C freezer.

When running the digested pGFP-rrnB plasmid DNA though the gel to extract the 8Kb fragment, we did not see the bands expected to be seen. Therefore another restriction enzyme digestion of the pGFP-rrnB DNA with EcoRI and NheI was attempted (with different concentrations of the enzymes and DNA). In addition more pGFP-rrnB DNA was digested but with EcoRI and NheI separately. All of the resulting digests were stored in the -20C freezer.

In today's experiments we hope to run 10ul of pGFP-rrnB treated with EcoRI and 10ul of pGFP-rrnB + NheI on some agarose gel for analysis. Additionally, 5ul of the 8Kb pGFP-rrnB digest fragment should be run on the gel.