Team:University of Lethbridge/Notebook/Protocols

From 2008.igem.org

Revision as of 02:27, 30 October 2008 by Munima.alam (Talk | contribs)

Back to The University of Lethbridge Main Notebook

Contents

PCR protocols

CheZ (Taq pol)

From September 28, 2008 in the "Chemotaxis" lab book:

- Tempate DNA 1uL
- 10X Econo Taq Buffer 2.5uL
- dNTP mix 1uL 
- Primer 1 5uL
- Primer 2 5uL
- Econo Taq 0.25uL
- ddH2O 19.75uL

Cycling Conditions:

- Incubate PCR Reactions 2 min at 94 C 
- Denature 30 sec at 94 C 
- Anneal 30 sec at 47 C 
- Extend 1 min/kb at 72 C 
- Final extension 7 min at 72 C 
- Hold indefinitely at 4 C 

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 (Taq pol)

From October 14, 2008 in the "Riboswitch" notebook: Objective: PCR of the riboswitch in a 50 uL x 9 reactions.

Master Mix (1x):

-10x Buffer: 5 uL
-10 mM dNTP: 1 uL
- 50 mM MgCl2: 1.5 uL
- 10 mM reverse primer: 1 uL
-10 mM forward primer: 1 uL
-Taq polymerase: 0.2 uL
-d2H2O: 39.3 uL

rspA TIR (Taq pol)

From September 30, 2008 in "rpsa TIR" notebook

Reaction Conditions:

 - 1.0 uL Template DNA
 - 5.0 uL 10x Buffer
 - 2.0 uL 10 mM dNTPs
 - 1.0 uL Forward Primer
 - 1.0 uL Reverse Primer
 - 0.5 uL Econo taq polymerase
 - 39.5 uL Optima H2O

Cycling Conditions:

1. 94 C 2 min
2. a. 94 C 15 sec
   b. 47 C 15 sec
   c. 72 C 15 sec 
3. Repeat step 2 for 25 cycles
4.72 C 5 min

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.

Other Protocols

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 3 gel volume 0.3 M NaAc (pH 7.0) at room temperature for 30 minutes.

-Make your own spin column from a small microfuge tube with a hole cut out of the bottom, involves flamage 
and a wire, stuff 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 95% 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 air dry for 10 minutes, this allows all ethanol to evaporate off.

-Resuspend in TE Buffer (pH 8.0), 10 uL.

-Quantify either by Gel or UV Spec.

-Proceed with ligation.