Difference between revisions of "Team:CSU Fort Collins/Experiments"

Materials

• Template DNA
• 5X HF Phusion Buffer or 10X HF Taq Buffer
• Molecular Grade Water
• dNTPs
• Primers
• DNA Polymerase (Phusion or Taq)

Procedure

Piece Amplification

1. Create the following mixture:

Component	50μl reaction
Molecular grade H2O	Added first. 32.5μL
5x HF Buffer	10μL
10 mM dNTPs	1.0μL
Primer A (10μM)	2.5μL
Primer B (10μM)	2.5μL
Template DNA	1.0μL
DNA polymerase	Added last. 0.5μL

2. Run the PCR reaction in the Thermalcycler with Thermalcycler Program as follows:

Cycle Step	Temp(C)	Time	Cycles
Initial denaturation	98	5 min	1
Denaturation	98	10s	35
Annealing	LowerTm+3	15s	35
Extension	72	45s/kb	35
Final Extension	72	10min	1
Hold	4	Hold	1

Colony PCR

1. Create the following mixture:

Component	50μl reaction
Molecular grade H2O	Added first 33.5ul
5x Phusion HF Buffer	10μL
10 mM dNTPs	1.0μL
Primer A (10μM)	2.5μL
Primer B (10μM)	2.5μL
Colony	1
Phusion DNA polymerase	Added last. 0.5μL

3. Run the PCR reaction in the Thermalcycler with Thermalcycler Program as follows:

Cycle Step	Temp(C)	Time	Cycles
Initial denaturation	98	5 min	1
Denaturation	98	10s	35
Annealing	LowerTm+3	15s	35
Extension	72	45s/kb	35
Final Extension	72	10min	1
Hold	4	Hold	1

Materials

• 2 LB + Antibiotic plates
• Spreaders or glass beads
• LB Media
• Ligated back bone
• Digested back bone(control)

Procedure

2. Digest your mixture in a water bath at 37C for 60min

Ligation Using the “Ligation Template” excel sheet, calculate the amount of each component to combine in a ligation mix for an Insert: Backbone ratio of 4:1

Incubate at 16C overnight on a heating block or at room temperature for 1 hour.

Materials

• 2 LB + Antibiotic plates
• Spreaders or glass beads
• LB Media
• Ligated back bone
• Digested back bone(control)

Procedure

1. Set water bath to 42C
2. Remove LB+Antibiotic plates from 4C and allow them to come to RT.
3. Thaw chemically competent cells on ice. Leave in microcentrifuge tube.
4. Add 5μL of ligation mix chemically competent cells.
5. Add 5uL of digested back bone to chemical competent cells as a control
6. Incubate on ice for 30 min.
7. Heat shock cells for 60 sec at 42C without shaking.
8. Aseptically (by the fire or in the hood) add 250μL of LB media to the tube (DO NOT ADD ANTIBIOTIC AT THIS STEP). Cap tightly.
9. Place tube horizontally in shaker. Incubate at 37oC and 225 rpm for 1 hr.
10. In the laminar hood, spread 100uL of transformants onto LB+Antibiotic plates.
11. Leave plates in 37C incubator overnight. Store remaining liquid cultures in 4oC.

LB Media

Material

• LB Miller (Powder)
• 1L Glass Bottle
• Stir Bar
• DI/RO Water

Procedure

1. Triple rinse bottle with DI water
2. Add stir bar to the bottle
3. Add 700 mL of DI Water to the 1L Bottle
4. Add 17.5 g of LB Miller
5. Put of stir plate and stir until large clumps are dissolved (Remaining small clumps will dissolve in Autoclave)
6. Tighten the cap all the way and loosen with 2 full turns to the left [IMPORTANT for SAFETY]
7. Place autoclave tape on top
8. Autoclave on Liq 30
9. Let cool and then tighten the cap and store at room temperature

LB Agar Media for Plates

Material

• LB Miller (Powder)
• 1L Glass Bottle
• Stir Bar
• DI/RO Water
• Agar
• Antibiotic if applicable
• Petri Dish Plates
• Ethanol Proof Markers
• Tape

Procedure

1. Triple rinse bottle with DI water
2. Add stir bar to the bottle
3. Add 700 mL of DI Water to the 1L Bottle
4. Add 17.5 g of LB Miller
5. Add 8.4g of agar (not agarose)
6. Put of stir plate and stir until large clumps are dissolved (Remaining small clumps will dissolve in Autoclave)
7. Tighten the cap all the way and loosen with 2 full turns to the left [IMPORTANT for SAFETY]
8. Place autoclave tape on top
9. Autoclave on Liq 30
10. Remove IMMEDIATELY from autoclave when finished
11. Place on stir plate and slowly stir (no air bubbles from stirring too fast) until the bottle can be held comfortable for a 7 seconds (20-30 min of cool down time)
12. Add 700 μL of aliquoted Antibiotic
13. INSIDE THE HOOD:
    1. Spray the sleeve of plates, the agar media, the marker, and the tape down with ethanol before putting them in the hood. When opening the sleeve of plates, be careful to not rip it because you will put the plates back into it.
    2. Following sterile technique pour the plates about a 3rd of the way full
    3. Allow to cool in the hood until they have solidified and are no longer warm
    4. Turn the plates upside down and put back in the sleeve
    5. Tape the sleeve shut and write the antibiotic and the date they were made on the tape.

Materials

• Agarose
• 1X TAE Buffer
• Parafilm
• Electrophoresis chamber and power source
• SYBR Green
• Loading Dye
• DNA Ladder
• PCR Samples

Procedure

1. Using a balance, mass out 0.5 gram of agarose (for 1% gel, for 2% mass out 1.0 gram). Mix this with 50 mL of TAE 1X Buffer.
2. Microwave the mixture, mixing by swirling intermittently, until all the agarose is dissolved and the mixture is homogeneous and clear (about 2 minutes).
3. Pour the mixture into a gel plate and insert a correctly-sized comb (8, 10, etc. lanes). Allow to cool and solidify on the benchtop.
4. Mix your samples on a piece of parafilm. Use 10 μL of the appropriate DNA Ladder (1 kb, 100 bp, 2 log, etc.) combined with 1 μL SYBR Green/DMSO in the first lane. For all samples, mix 10 μl of sample and 2 μL of SYBR Green/Dye Mixture.
5. Place gel in tray into the gel electrophoresis apparatus - wells should be close to the negative (conventionally black) end. Fill apparatus with 1X TAE until the gel is completely submerged. Do not overfill - there is a guide sticker on the apparatus which marks the max fill line.
6. Load 10 μL of each sample into the appropriate wells.
7. Connect wiring and run gel electrophoresis at 110 V for 1 hour.
8. Analyze gel in UV light and see if samples match the expected size using the ladder as a guide.

Materials

Procedure

1. First
2. Second
3. Third

Materials

• Experimental strains
• LB
• Chloramphenicol
• LB Powder
• Glucose
• IPTG
• DI water
• Shake flasks
• Syringe filter
• Quartz cuvettes
• 50 mL centrifuge tubes

Procedure

1. Create two different strains of E. coli to compare.
   
   • Strain 1: DH5Α E. coli with lac promoter
   • Strain 2: DH5Α E. coli with lac promoter and genes of interest
2. From glycerol stock, create three 2 mL overnight cultures in LB of each E. coli strain (total of six cultures. Incubate at 37 degC and 225 rpm overnight
3. Prepare solutions and glassware
• Make 150 mL stock solution of glucose at 200 g/L
• Make 225 mL stock solution of LB media (7.5 g in 225 mL)
• Make 10 mL stock solution of IPTG at 1 M
4. Autoclave six 250 mL shake flasks, the LB, and the glucose stock solutions using a Liquid 30 cycle
5. Prepare 50 mL of media in shake flasks
• 12.5 mL of glucose solution at 200 g/L for a concentration of 50 g/L
• 37.5 mL of LB media at >1X for a concentration of 1X
• 25 uL of IPTG solution at 1 M for a concentration of 0.5 mM
6. For each overnight culture, take an OD₆₀₀
7. Use C₁V₁ = C₂V₂ to calculate the volume of overnight culture required to inoculate the culture at OD₆₀₀ of 0.05
8. Incubate shake flasks at 37 degC and 225 rpm
9. Take OD measurements
• For the first six hours (starting at the first hour) take one 750 uL samples each hour
• Then take one 100 uL sample every 12 hours until the total incubation time reaches 72 hours
• Measure each sample in the OD reader at 600 nm; for the 100 uL samples, dilute them 1:10 with 900 uL of blank solution before measuring
10. At the end of the experiment, remove 1 mL of suspension from each flask and store in a microcentrifuge tube to use for HPLC analysis
11. Remove 25 mL of suspension from each flask and store in a 50 mL centrifuge tube
• Spin down cells at 5000 x g for 15 minutes
• Transfer supernatant to another 50 mL centrifuge tube
• Store cells and liquid at -80 degC

Materials

• First
• Second
• Third

Procedure

1. First
2. Second
3. Third

Materials

• First
• Second
• Third

Procedure

1. First
2. Second
3. Third