Calgary/protocols

• Full Procedure
• Protocols and Techniques
• Parts and Primers
• Printer System
• Results

Bacterial Transformation

• Thaw 100 ul of competen cells (per transformation) on ice just before they are needed
• Add DNA (max 20ul) thawed cells and mix by flicking the side of the tube. Leave on ice for 30 minutes
• Heat shock for 2 minutes at 42 degrees Celsius or 5 minutes at 37 degrees Celsius
• Place on Ice for 5 minutes
• Add 250ul SOC medium to each tube
• Incubate for 30 to 60 minutes with shaking at 37 degrees Celsius. (Note that for Kanamycin containing plasmides always use one hour)
• Spin down to remove all supernatant except approximately 100 ul
• Plate approximately 30 ul on each of two antibiotic plates
• Grow overnight at 37 degrees Celsius

For this protocol we used three controls

• Positive Control - pBluescript in TOP10 cells on amp resistant plates
• Negative Control - TOP10 cells grown on amp resistant plates
• Negative Control - DB31 cells on amp resistant plates

Rehydration

Biobrick parts are shipped from the registry in a dehydrated from. As such they must be rehydrated before they can be used.

• Puncture a hole through the foil with a pipette tip into the well that corresponds to the Biobrick - standard part that you want
• Add 15 ul of diH20 (deionized water)
• Take 1 ul DNA and transform into your desired competent cells, plate out onto a plate with the correct antibiotic and grow overnight. Your goal here is to obtain single colonies

For this protocol we used three controls

• Positive Control - pBluescript in TOP10 cells on amp resistant plates
• Negative Control - TOP10 cells grown on amp resistant plates
• Negative Control - DB31 cells on amp resistant plates

PCR Protocol

Thermocycler Conditions

• 1 Cycle - 6 minutes at 95 degrees Celsius
• 36 cycles
  • 1 minute at 95 degrees Celsius
  • 1 minute at 58 degrees Celsius ( this step done at 65 degrees Celsius for higher GC content )
  • 1 minute at 72 degrees Celsius
• 1 Cycle - 10 minutes at 72 degrees Celsius then HOLD at 4 degrees Celsius

Conditions were varied as needed. For example in cases of longer products all 1 minute times were increased to 1.5 to 3 minutes

Plasmid Preparation Protocol - from GenElute Plasmid Miniprep Kit

• Harvest Cells
  • pellet 1-5 ml of an overnight culture.
• Resuspend Cells
  • Completely resuspend the bacterial pellet with 200ul of resuspension solution. Vortex or pipette up and down to throroughly resuspend cells until homogenous. Incomplete suspensions will result in poor recovery.
  • Another rapid way to resuspend the cell pelles is to scrape teh bottoms of the microcentrifuge tubes back and forth five times across the surface of a polpropylene microcentrifuge tube storage rack with 5 X 16 holes
• Lyse Cells
  • Lyse resuspended cells by adding 200 ul of the lysis solution. Immediately mix the contents by gentle inversion (6-8 times) until the mixture becomes clear and viscous. Do Not Vortex .
• Neutralize
  • Precipitate the cell debris by adding 350 ul of the Neutralization/Binding solution. Gently invert the tube 4-6 times. Pellet the cell debris by centrifuging at maximum speed for 10 minutes.
• Prepare Column
  • Insert a GenElute Miniprep Binding Column into a provided microcentrifuge tube, if not already assembled. add 500 ul of the Column Preparation Solution to each miniprep column and centrifuge at Max speed for 30 to 60 seconds. Discard the flow through liquid.
• Load Cleared Lysate
  • Transfer the cleared lysate from step 4 to the column prepared in step 5 and centrifuge at Max speed for 30 to 60 seconds. Discard the flow through
• Wash Column
  • Add 750 ul of the diluted Wash Solution to the column. Centrifuge at Max speed for 30 to 60 seconds. The column wash step removes residual salt and other contaminants introduced during the column load. Discard the flow through liquid and centrifuge again at maximum speed for 1 to 2 minutes without any additional wash solution to remove excess alcohol
• Elute DNA
  • Transfer the column to a fresh collection tube. Add 100ul of Elution Solution or molecular biology reagent water to the column. For DNA sequencing and other enzymatic applications, use water or 5mM tris-HCL, pH 8.0, as an eluant. Centrifuge at Max speed for 1 minute. DNA is now present in the eluate and is ready for immediate use or storage at -20 degrees Celsius.

Construction Technique

Determine the order of the two parts you will be putting together; the one in front will be referred to as the insert, while the one behind will be referred to as the vector. Both the vector and the insert need to have their own separate tube, at least in the beginning.

Restriction Digest Protocol

In the Insert Tube...

• 600ng of DNA (To figure out the volume, the calculation is 600 / concentration of plasmid. This gives you volume in μL).
• Water, so that the volume of DNA and water in the tube is 35 μL
• 4 μL of React 1 Buffer
• 0.5 μL of EcoR1
• 0.5 μL of Spe1

In the vector Tube...

• 250ng of DNA (To figure out the volume, the calculation is 250 / concentration of plasmid. This gives you volume in μL).
• Water, so that the volume of DNA and water in the tube is 35 μL
• 4 μL of React 2 Buffer
• 0.5 μL of EcoR1
• 0.5 μL of Xba1

Put both tubes into the 37°C water bath for one hour. After, place them into the 65°C heating block for 10 minutes. This destroys any enzymes in the tube (which is ok, because by now they’ve done all they need to). Take the insert out, and put it in a -20°C freezer.

Antarctic Phosphatase Protocol

To the vector tube, add 5 μL of 10x Antarctic Phosphatase Buffer, 4 μL of water, and 1 μL of Antarctic Phosphatase. We do this to prevent the vector from closing up again without any insert. Put the tube into the 37°C water bath for 30 mins. After, place it in the 65°C heating block for 10 minutes.

Ligation Protocol

Take the insert out of the freezer, and add 5 μL of insert and 5 μL of vector to a new tube. Label the rest of each tube as Unligated, put the date on the tube, and stick it in the -20°C freezer incase your transformation doesn’t work. To the single tube of 10μL mix, add 10 μL of 2x Quick Ligase Buffer, and 1 μL of Quick Ligase. Let this sit at room temperature for 5 minutes.

You are now done. If you are going to transform this construction product, add all 21μL to a tube of whatever bacteria you're using.

Vector Dephosphorylation with Antarctic Phosphatase

Vector Dephosphorylation with Atlantic Phosphotase Protocol

Ensure that restriction enzyme has been heat inactivated by heating tube in 37°C water bath for one hour. Then place into a 65°C heating block for 10 minutes. This destroys any remaining enzymes in the tube.

• Add 1/10 volume of 10x Antarctic Phosphatase Reaction Buffer to 1 ug of DNA cut with any restriction endonuclease in any buffer.
• Add 1 μl of Antarctic Phosphatase (5 units) and mix.
• Incubate for 15 minutes at 37°C for 5´ extensions or bluntends, 60 minutes for 3´ extensions. Note: for typical iGEM restriction digests use one hour.
• Heat inactivate for 5 minutes at 65°C (or as required to inactivate the restriction enzyme).

LB - Agar Plate Preparation Protocol

• Weigh 35g of LB-Agar powder mix per litre of media desired. One litre makes 40-50 plates
• Select an appropriate flask; the lab autoclave will cause flasks half full and above to boil over! Use a 2L flasks for up to .5 L of media, a 4 litre flask for up to 1.5L, etc
• Disolve LB-Agar, using water from one of the wall mounted nanopure filters. Add a stir bar and use a magnetic stirrer to speed things up
• Cover the flask with aluminum foil, and secure the foil with autoclave tape. The foil should be somewhat loose (to avoid building pressure in the flask while sterilizing and blowing the foil off), but not so loose that lots of liquid can escape
• Put the flask in a plastic autoclave tray, load into the autoclave, and sterilize using the 20 minute liquid program
• Once the autoclave finishes venting (which can take twice as long as the sterilization proper), check that the foil covering is still in place. If it is not, the media is contaminated! Unload using the insulated oven gloves
• Allow the media to cool until it can be handled without the oven mits. The cold room can be used to speed this up. Alternatively, if a large batch of media is prepared flasks may be kept hot in the prep lab water bath, to avoid all of them cooling at once. Agar polymerization cannot be reversed once it starts (and if it begins to set in the flask you're in trouble!), but media can be kept from setting further by keeping it hot.
• Once media is cool, add other desired ingredients. Use the magnetic stirrer to mix, but do NOT add a stir bar now, or the media will be contaminated. (If one wasn't added before, you must do without.) Common additions include:
  • ampicillin (stock 100mg/ml, final 100ug/ml)
  • kanamycin (stock 50mg/ml, final 50ug/ml)
  • chloramphenicol (stock 50mg/ml, final 30ug/ml)
  • x-gal (stock 40mg/ml, final 40ug/ml)
  • To achieve final concentrations, add 1mL of stock per 1L of media, except for chloramphenicol, where 0.6mL per 1L of media is added instead
• Pour directly from the flask into sterile petri plates. Use a quick pass with a bunsen burner flame to snuff out bubbles that form during pouring. Do not subject the plate to continuous heat or the plate will melt, and the heat sensitive ingredients added in the previous step will be destroyed. Bubbles can allow cells to access nutrients without being exposed to the plate's antibiotic, and should be blown out immediately before the gel can set. It's a good idea for one person to pour while another flames bubbles.
• Allow the plates to stand right side up overnight, or until the gel sets if they are needed sooner. Plates should be stored upside down to keep condensation from falling on the media. Store petri plates in the plastic bags they ship in, in the 4 degree cold room.