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Week 7
Monday, 16-Aug-2010
- midi-prepped the XylE-transformed E.coli. The DNA yeild from the midi-prep was 134micrograms as determined by spectrophotometry. This is the XylE that is going to be used for all further experiments.
- restriction digestion of midi-prepped XylE by Xbal and PstI to prepare it for 3A assemply. (with J23101 promoter and PSB1C3 vector)
- gel analysis of the restriction digestion mixture to isolate XylE gene
Midi-prep XylE digestion with xbaI and PstI The smaller size bands at lanes 2 & 3 are the ones that are going to be cut out and used in gel purification to extract the XylE gene (with sticky ends for XbaL and PstI).
▪ I made an overnight culture of Bacillus
Tuesday, 17-Aug-2010
- using the Gel Extraction Kit, we isolated the restriction enzyme cut XylE gene from the agarose gel lamp.
- gel analysis of XylE, J23101 promoter and pSB1C3 vector samples to determine their ratios for 3A assemply ligation
- 3A assemply of XylE, J23101 promoter and pSB1C3 vector.
- Transformation of XL-Blue competent E.coli with the above construct.
gel analysis of XylE, J23101 promoter and pSB1C3 vector samples to determine the volume ratios of samples to be used for 3A assemply ligation
- I followed Chris's Bacillus transformation protocol to transform Bacillus with constitutive GFP and RFP DNA as well as a control without DNA
Thursday, 19-Aug-2010
- We run the XylEGFP1 PCR reaction to construct the His-GFP-Flag and Linker-XylE-Spe construct.
Friday, 20-Aug-2010
The J23101 gene in a biobrick vector containg RFP gene
- we run a gel on XylEGFP1 PCR reaction. Results: GFP was extended successfully, XylE extension FAILED (too much non-specific annealing)
- catechol assay on 2hrs bench ligation of promoter,xylE and vector failed.
- two replica plates of overnight ligated J23101, XylE and pSB1C3 transformed E.coli (one for catechol assay)
- the His-GFP-Flag DNA was gel purified
- transformation of XL-1Blue cells with J23101 in J62001 vector from the registry. One more attemp to construct a successful promoter-xylE ligation, since we believe that the strand annealed promoter was of bad quality
Week 8
Monday, 23-Aug
- set up overnight cultures for midi-prep
- gel separation of linker-XylE-Spe DNA FAILED
- PCR reaction for extension of His-GFP-Flag
- Catechol assay on E.coli transformed with overnight ligated J23101, XylE and pSB1C3. FAILED
Tuesday, 24th-Aug
- midi-prepped registry obtained J23101. A yield of 130ng/ul of promoter was obtained. The promoter is in a biobrick vector called J62001. The promoter is upstream of RFP gene.
- the vector carrying the promoter was digested with SpeI and PstI, while XylE gene was digested with XbaI and PstI.
- the promoter and the XylE gene were gel purified.
- a reaction between the promoter(still on vector) and XylE was set on for overnight ligation
- PCR purification of GFP2 -> GFP construct ready for full fusion protein.
- Gel purification of XylE lost DNA along the way. Thus PCR XylE1 with gradient for temperature scanning (taq): PCR round 1 included 62C and only rev primer to create pool of successful extensions with with rev primer (60-62). PCR round 2 with Fwd primer and temperature scale (68-68, 72-74).
Wednesday, 25th-Aug
Performed gel analysis on the purified XylE and J23101 to obtain ratios for ligation. First gel was scrapped as it produced appauling(explanation for Nick:really bad) results, 2nd gel run was successful.
- Performed a ligation reaction between the vector containing J23101, and XylE(one on bench and one overnight one).
- Transformation of the new plasmid into competent E.coli. Successfully transformed colonies can be selected for by loss of RFP expression.
- XylE-1 PCR with temperature cascade. Gel analysis and purification.
Thursday, 26th-Aug
- white colonies from the promoter-XylE transformed E.coli were picked and transferred to new amp plates. One is the replica plate and the other is the catechol assay plate.
- XylE-1, two rounds of PCR/purification were run to obtain a sufficiently clear band. An additional PCR run for XylE-1 was discarded afterwards.
Friday, 27th-Aug
- Catechol assay performed on promoter-XylE transformed E.coli. SUCCESSFULL
- XylE-2 PCR and gel-purification cycles (2x) to obtain clear band. XylE-2 is now ready for assembly of the GFP-XylE fusion protein.
Saturday, 28th-Aug
- Preparing the annealing step between the GFP-2 and XylE-2 constructs, we discovered sequence dissimilarities in the TEV-cleavable regions which we planned to use for the annealing step. Nevertheless a PCR was run with appropriate conditions (allowing for a minimal amount of unspecific annealing).
Sunday, 29th-Aug
- Gel analysis of the attempted annealing reaction of GFP-2 XylE-2 showed unsufficiently clear bands for gel-purification. A new reaction is being prepared: 10 rounds of annealing PCR, followed by addition of primers (5' primer for GFP-2 and 3' primer for XylE-2) in order to introduce an amplification step in the reaction. --- Following Kirstins advice, we are discarding this reaction and wait for the arrival of new primers for XylE-2 (5' + TEV) and GFP-2 (3' +TEV).
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