Team:University of Sheffield/Gosia

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16/08/08

Primers for Kan cassette synthesis ordered.

21/08/08

Primers arrive. Rehydration of a primers was carried as follows: volume a dH2O (uL) equal to ten times the number of nanomoles of DNA present in the tube will produce a stock solution at 100µM concentration.

Due to data corruption I do not have an electronic copy of my lab book any more. I am publishing my handwritten notes as an evidence of my work.

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24/10/08

BBs construction continues - a PCR was run to PCR-out genes cqsS, barA and Red Recombinase cassette. A PCR run yesterday by Rosie didn't work in all cases (Illustration 1).

The procedure was carried out in accordance with Protocol [X] except that 1 µl of 100 mM stock solutions of forward and reverse primers were used instead of 2 pm/µl as usually. 10 ng of plasmid pKD46 was added instead of 1 ng. Exact volumes of PCR reaction mixture components is listed in Table 1.

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PCR of BBs carried out by Rosie yesterday (23/10/08)

25/10/08

Plan for preparing BBs for shipment was established and first part of it carried out. BBs genes were purified for further digestion. However cleaned BBs weren't run on the analytical gel to save some time. They will be run tomorrow as digestion will change bands by size that agarose cannot resolve. The size estimated tomorrow will correspond to the size of the PCR products. DNA concentration in a sample was estimated to know how much of it to add to restriction digest mixture. Genes were restriction digested to generate sticky ends for further ligation with plasmid backbone.

Procedure for preparing BBs for shipment is as follows:

  • clean a PCR products
  • run the cleaned up products on the analytical gel
  • check what is the concentration of DNA in a sample
  • restriction digest BBs
  • clean the digest
  • run the analytical gel of the restriction digest
  • purify the BB plasmid from the gel [this resolves plasmid backbone and CcdB gene and prevents from

PCR was cleaned with QIAquick PCR purification kit from QIAGEN. Concentration of DNA in a sample was measured with spectrophotometer. Restriction digest was carried out as in the Protocol [X]. Genes were restriction digested with enzymes SpeI and EcoRI from NEB. Buffer used was NEB2 buffer from NEB. List of BBs genes and plasmids digested is given in a Table 1. Exact volumes of components of restriction digest mixture are listed in Table 2.

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