Characterization B: Expression of PHIX174 promoters fused to UTR1-deGFP.
- Reboot and starting construction over from scratch.
Characterization C: Expression of PHIX174 promoters fused to UTRX-deGFP.
- Reboot and starting construction over from scratch.
Hypothesis 2: Gene L is necessary for phage propagation.
- Need to design new primers (regular and mutagenic) for amplifying PHIX174 genome.
To do
- Today
- To create the following linkers:
- SphI-PA-NcoI linker
- SphI-PD-NcoI linker
- SphI-PF-NcoI linker
- Hydridize 2mM complimentary ssDNA oligonucleotides. Product is linker at 1mM concentration. Perform 1/10 serial dilutions to 100 nM final concentration.
- To initiate the following linkers:
- SphI-PB-NcoI linker
- SphI-PG-NcoI linker
- SphI-PL-NcoI linker
- SphI-PLPA-NcoI linker
- Perform PCR using ΦX174 genomic DNA as template.
- Follow with PCR purification. Elute with 100 μL H2O and speedvac to ~20 μL.
- Double digest overnight with SphI and NcoI.
- Today +1
- To obtain following linkers, perform Gel extraction (elute in 100 μL H2O, linkers should be at ~100nM concentration):
- SphI-PB-NcoI linker
- SphI-PG-NcoI linker
- SphI-PL-NcoI linker
- SphI-PLPA-NcoI linker
- To create the following linkers:
- SphI-PA-NheI linker
- SphI-PB-NheI linker
- SphI-PD-NheI linker
- SphI-PF-NheI linker
- SphI-PG-NheI linker
- SphI-PL-NheI linker
- Hydridize 2mM complimentary ssDNA oligonucleotides. Product is linker at 1mM concentration. Perform 1/10 serial dilutions to 100 nM final concentration.
- To initiate the following linkers:
- SphI-PLPA-NheI linker
- Perform PCR using ΦX174 genomic DNA as template.
- Follow with PCR purification. Elute with 100 μL H2O and speedvac to ~20 μL.
- Double digest overnight with SphI and NcoI.
- Today +3
- To obtain following linkers, perform Gel extraction (elute in 100 μL H2O, linkers should be at ~100nM concentration):
- SphI-PLPA-NheI linker
- The entire list of linkers is now as follows:
- SphI-PA-NcoI
- SphI-PB-NcoI
- SphI-PD-NcoI
- SphI-PF-NcoI
- SphI-PG-NcoI
- SphI-PL-NcoI
- SphI-PLPA-NcoI
- SphI-PA-UTRA-NheI
- SphI-PB-UTRB-NheI
- SphI-PD-UTRD-NheI
- SphI-PF-UTRF-NheI
- SphI-PG-UTRG-NheI
- SphI-PL-UTRL-NheI
- SphI-PLPA-UTRA-NheI
- SphI-NULL-NheI
- Verify that linker concentrations are all ~100nM with quantifluore DNA quantification.
- The list of backbones is:
- pBEST-SphI//NcoI-UTR1-deGFP-T500 (10nM). Ligate 0.5 μL with 5 μL SphI-PX-NcoI linkers.
- pBEST-SphI//NheI-deGFP-T500 (2nM) Ligate 0.5 μL with 5 μL SphI-PX-UTRX-NheI linkers.
- The entire list of ligation product constructs is now:
- pBEST-PA-UTR1-deGFP-T500
- pBEST-PB-UTR1-deGFP-T500
- pBEST-PD-UTR1-deGFP-T500
- pBEST-PF-UTR1-deGFP-T500
- pBEST-PG-UTR1-deGFP-T500
- pBEST-PL-UTR1-deGFP-T500
- pBEST-PLPA-UTR1-deGFP-T500
- pBEST-PA-UTRA-deGFP-T500
- pBEST-PB-UTRB-deGFP-T500
- pBEST-PD-UTRD-deGFP-T500
- pBEST-PF-UTRF-deGFP-T500
- pBEST-PG-UTRG-deGFP-T500
- pBEST-PL-UTRL-deGFP-T500
- pBEST-PLPA-UTRA-deGFP-T500
- pBEST-NULL-deGFP-T500
- Today +4
- Transform the ligation products into JM109 competent cells and grow overnight (15 plates).
- Today +5
- Select 4 colonies per plate and grow 2.5 mL miniculures (4 × 15 = 60 total).
Notes
Recently Edited Notebook Pages
Digital Signature
- SC 11:50, 29 June 2012 (EDT):
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