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Team:University of Lethbridge/Notebook/Protocols
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Contents |
PCR protocols
CheZ (Taq pol)
CheZ (Phusion pol)
Conditions for one reaction (25 uL):
-1x HF buffer (5 uL 5x buffer) -Forward primer (1.5 uL) -Reverse primer (1.5 uL) -dNTPs (0.5 uL) -Phusion (0.25 uL) -mQH2O (15.25 uL) -Template (1 uL)
Cycling protocol ("cheZ"):
1. Initial denaturation @ 98C for 4 mins (1 cycle) 2a. Denaturation @ 98 C for 30 sec (35 cycles for step #2) b. Annealing 47.0C for 30 seconds c. Extension @ 72C for 30 sec 3. Final extension @ 72C for 7 mins (1 cycle) 4. Hold at 4C
Riboswitch
rspA TIR
Other protocols
xylE PCR (with Phusion pol.) Master Mix for 1 reaction (50 uL):
- 10x Buffer: 5 uL - 10 mM dNTPs: 1 uL - 50 mM Mg2+: 1.5 uL - 10 uM RF: 1 uL - 10 uM RR: 1 uL - Phusion polymerase: 0.2 uL - H20: 39.3 uL - template: 1 uL
Cycle conditions "xylE":
1. Denaturation: 94 C for 1 min 2. a. Denaturation: 94 C for 30 seconds b. Annealing: 52 C for 30 seconds c. Extension: 70 C for 30 seconds Repeat Step 2 for 30 cycles 3. Final extension: 72 C for 10 minutes, then hold at 4 C.
Competency
Squeeze 'n Freze Gel Extraction
-Run the sample you wish to extract on a TAE-Agarose Gel -Cut out the band you wish to purify -Incubate in 1 gel volume 0.3 M NaCOOH at room temperature for 30 minutes. -Make your own spin column from a small microfuge tube with a hole cut out of the bottom, stuffed with glass wool. This tube should be inserted inside a 1.5 mL microfuge tube. -Transfer the solution to the spin column. -Freeze the tube in liquid Nitrogen for 1 minute, then spin at full speed for 15 minutes. -Precipitate the DNA in Ethanol. Remove the supernatant. -Wash in 75% Ethanol. Remove as much ethanol as possible. -Centrifige for 5 minutes then, remove the rest of the ethanol. -Let pellet to air dry for 10 minutes, this allows all ethanol to evaporate off. -Resuspend in TE Buffer, 10 uL. -Quantify either by Gel or UV Spec. -Proceed with ligation.
