IGEM:UNAM/2009/Notebook/Modeling logbook Claudia/2010/08/21
 UNAM-Genomics-Mexico team
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Working on LuxY synthesized plasmid from Mr.GeneIn order to test the correct lenght of LuxY synthesized, I am going to do a PCR reaction using as template the plasmid harboring LuxY from Mr.Gene. Primers: Forward:Preffix primer Reverse:Suffix primer
Plasmid harboring LuxY from Mr.Gene
Working on LovTAP promoters:Dephosphatation of strong,medium and weak promoters for ligationOnce the plasmids harboring the seven promoters were correctly digested with the enzymes SpeI and PstI, I have started the dephosphatation reaction for each one in order to prepare them for ligation.
1.Incubate the samples at 37°C during 20 min. 2.Incubate the samples at 65°C during 10 min
Results: Dephosphatation of strong, medium and weak promoters for ligation with LovTAP Working on LovTAP: Extraction from gel bandIn order to extract LovTAP from the gel ready for ligation with J23 promoters and plasmid pSB1C3, I'm going to use the gel extraction Kit from QIAGEN. The extraction of LovTAP from gel was decided considering the results previously reported, which are found in the next link. Gel extraction protocol1. Prepare the gel using low melt agarose at 1%.
2. Run the gel in cold room. 3. Follow the gel extraction protocol from QIAGEN
The samples used to run the gel were:
These were obtained previously. Resuts: LovTAP Gel extraction protocolWe were only able to extract LovTAP from colony 1 digested with XbaI and PstI, the sample digested with EcoRI and PstI was lost during the gel loading step. After the extraction we ran the sample in a new gel, in order to know if the gel extraction was done correctly. In lane 6 of the next image I loaded LovTAP extracted from colony 1 and digested with XbaI and PstI. There is a band around the expected size (889nt) for LovTAP, but there is another weak band down LovTAP, thus the LovTAP extaction from gel has a little contamination from other digested product. Despite this contamination we decided to continue with the ligation procedure in order to join LovTAP with the choosen promoters. So that, I also loaded the plasmids harboring the promoters that were digested and dephosphated for ligation -Lane 7 to Lane 13- to calculate the quantity of the samples that must be used for ligation. 
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