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Contents 1 LB Agar 2 Adding Antibiotics to LB 3 SOB Media Recipe 4 SOC Media Recipe 5 Creating Chemically Competent Cells 6 Transforming Chemically Competent Cells 7 Miniprep Procedures 7.1 Original Miniprep Procedure 7.2 Alterations to Miniprep Procedure (as of June 19) 8 PCR protocol 9 3A Assembly 10 Gibson Assembly 11 Silica Creation

LB Agar

• We used a premade [http://www.bd.com/ Becton, Dickinson and Comapny] mix to make our [http://www.bd.com/ds/productCenter/244520.asp LB agar].

Adding Antibiotics to LB

• How to make LB liquid plus antibiotics:
  • Ampicillin – The frozen stock solutions of ampicillin are at 50mg/ml and 100mg/ml in H2O, and are marked with a red sticker. The final concentration for LB liquid culture is 50ul/ml. To obtain this in 100ml (the amount in each LB bottle), add 100ul stock solution.
  • Kanamycin – The frozen stock solutions of kanamycin are at 50mg/ml in H2O, and are marked with green. The final concentration for LB liquid culture for growing plasmids is 50ug/ml, and for cosmids is 20ug/ml. To obtain 50ng/ml in 100ml of LB, add 100ul stock solution, and to obtain 20ug/ml, add 40ul stock solution.
  • Tetracycline – The frozen stock solutions of tetracycline are at 15mg/ml in methanol and are marked with black. The final concentration for LB liquid culture is 15ug/ml. To obtain this in 100ml of LB, add 100ul stock solution.
  • Chloramphenicol – The frozen stock solutions of chloramphenicol are at 25mg/ml in 100% ethanol and are marked with purple. The final concentration for LB liquid culture is 25mg/ml. To obtain this in 100ml of LB, add 100ul stock solution.

• How to make LB plates plus antibiotics:
  • Follow the recipe card in box for making LB plates, being sure to add the agar. After autoclaving, and when the agar has cooled enough that it’s not too hot to touch (about 1 to 1.5hrs), add antibiotics as follows:
  • Ampicillin – add 1ml ampicillin (at 100mg/ml) per liter of agar to obtain a final concentration of 100ug/ml. Mark the plate with a single red line on the side.
  • Kanamycin – add 1ml kanamycin stock (at 50mg/ml) per liter of agar to obtain a final concentration of 50ug/ml. Mark the plates with a single green line on the side.
  • Tetracycline – add 1ml tetracycline stock (at 15mg/ml) per liter of agar to obtain a final concentration of 15ug/ml. Mark the plates with a single black line on the side.
  • Chloramphenicol – add 1ml chloramphenicol stock (at 25mg/ml) per liter of agar to obtain a final concentration of 100ug/ml. Mark the plates with a single purple line on the side.

SOB Media Recipe

• 2% w/v bacto-tryptone (20 g)
• 0.5% w/v Yeast extract (5 g)
• 8.56mM NaCl (0.5 g) or 10mM NaCl (0.584 g)
• 2.5mM KCl (0.186 g)
• ddH2O to 1000 mL[4]

• For maximum effectiveness, SOB media should have its pH adjusted to 7.0 by adding concentrated sodium hydroxide.
• Autoclave media to ensure sterility

SOC Media Recipe

In addition to the contents of SOB media

• 10mM MgCl2 (0.952 g) or 20mM MgSO4 (2.408 g)[2]
• 20mM glucose (3.603 g)
• Alternatively, SOC can be made by adding small amounts of concentrated magnesium chloride and glucose solutions to pre-prepared SOB.

• For maximum effectiveness, SOC media should have its pH adjusted to 7.0 by adding concentrated sodium hydroxide.
• Autoclave media to ensure sterility

Creating Chemically Competent Cells

• The protocol for creating chemically competent cells is provided by the parts registry and can be found [http://partsregistry.org/Help:Protocols/Competent_Cells here].

Transforming Chemically Competent Cells

• The protocol for transforming chemically competent cells is provided by Open Wet Ware and can be found [http://openwetware.org/wiki/Transforming_chemically_competent_cells here].

Miniprep Procedures

• For this procedure, we used the [http://www.qiagen.com/products/plasmid/qiaprepminiprepsystem/qiaprepspinminiprepkit.aspx#Tabs=t0 QIAprep Spin Miniprep Kit] by [http://www.qiagen.com/default.aspx Qiagen].

Original Miniprep Procedure

1. Add 1.5mL of overnight culture to a micorcentrifuge tube
2. Spin for 3 minutes at 800rpm
3. Decant the supernatant so that the DNA pellet is all that remains
4. Repeat steps 1-3 three times
5. Add 250μL of buffer P2 and invert several times to mix (do not allow the solution to sit for more than 5 minutes)
6. Add 300μL of buffer N3 and immediately invert to mix
7. Centrifuge at 13,000rpm for 10 minutes
8. Apply the supernatant to the QIAprep spin column by decanting or pipetting
9. Centrifuge at 13,000rpm for 1 minute and discard flow through
10. Wash the QIAprep spin column by adding 500μL buffer PB
11. Centrifuge at 13,000rpm for 1 minute and discard flow through
12. Wash the QIAprep spin column by adding 750μL Buffer PE
13. Centrifuge at 13,000rpm for 1 minute and discard flow through
14. Centrifuge at 13,000rpm for 1 minute
15. Place the QIAprep column in a clean 1.5mL microcentrifuge tube
16. Elute the DNA by adding 50μL of Buffer EB to the center of the QIAprep spin column
17. Let stand for 1 minute
18. Quantify DNA concentration with nanodrop

Alterations to Miniprep Procedure (as of June 19)

1. The P2 and N3 steps (steps 5 and 6) were done twice
2. The final elution (step 16) was completed using 50°C nanopure water

PCR protocol

1. For a 25ul rxn:
   • Use 1ul of 60ng/ul or 100ng/ul DNA
   • Use 1ul of each primer at 3.2pmole/ul concentration or 1.25ul of each primer at 100ng/ul concentration
   • 2.5ul 10x PCR Buffer w/ Mg (1.5mM)
   • 0.5ul 25mM MgCl2
   • 0.5ul dNTP
   • 0.125ul Taq
   • 18.375ul sterile water to equal a 25ul rxn
   • if not making master mix, dilute Taq so that you can add 1ul of Taq and 17.5ul sterile water to equal a 25ul rxn
2. For a 50ul rxn:
   • Use 2ul of 60ng/ul or 100ng/ul DNA
   • Use 2ul of each primer at 3.2pmole/ul concentration or 2.5ul of each primer at 100ng/ul concentration
   • 5ul 10x PCR Buffer w/ Mg
   • 1ul 25mM MgCl2
   • 1ul dNTP
   • 0.25ul Taq
   • 36.75ul sterile water to equal a 50ul rxn
   • if not making a master mix, dilute Taq so that you can add 1ul of Taq and 36ul sterile water to equal a 50ul rxn
3. Keep the reagents on ice.
4. Add the Taq last, and keep it in the freezer until you are ready to add it.
5. Vortex briefly and quick spin.
6. Cycle:
   • 95°C for 1-5minutes (usually 4min)
   • 95°C for 1min
   • 55°C for 1min. Cycle 30 times
   • 72°C for 1.5 to 2min (usually 2min)
   • 72°C for 10min
   • 4°C hold

• A video showing the theory behind PCR can he found [http://www.youtube.com/watch?v=HMC7c2T8fVk&feature=fvwrel| here]

3A Assembly

• The protocol for 3A assembly is provided by Open Wet Ware and can be found [http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly here]

Gibson Assembly

Prepare a master mix, as detailed below. Store them in 15 ul aliquots at -20 °C. Then:

1. Thaw a 15 μl assembly mixture aliquot and keep on ice until ready to be used.
2. Add 5 μl of DNA to be assembled to the master mixture. The DNA should be in equimolar amounts. Use 10-100 ng of each ~6 kb DNA fragment. For larger DNA segments, increasingly proportionate amounts of DNA should be added (e.g. 250 ng of each 150 kb DNA segment).
3. Incubate at 50 °C for 15 to 60 min (60 min is optimal).
4. [http://openwetware.org/wiki/Transforming_chemically_competent_cells Transform] as usual

• The protocol for Gibson assembly is provided by Open Wet Ware
• The original paper for the Gibson assembly protocol can be found [http://www.nature.com/nmeth/journal/v6/n5/pdf/nmeth.1318.pdf here]

Silica Creation

1. Obtain 14.4g of nanopure water
2. Obtain 50µL of .04M HCL and combine it with the water. Put this solution in an ice bath
3. Obtain 7.6g of tetramethyl orthosilicate (TMOS) in a separate container
4. Combine the TMOS and HCL/water
5. Immediately begin the vortex the solution. The solution will be cloudy while the reaction is taking place. Once the solution is clear again, the reaction is finished. This will take approximately 5 minutes
6. When the reaction is finished, let the solution set for 1-2 minutes
7. Use a rotary evaporator at 47ºC to remove the methane from the solution. This should take 2-3 minutes. The final solution volume should be approximately 13mL
8. If the silica is to be used immediately, put it on ice. It can be stored for up to a week if it is refrigerated.
9. Filter the silica before use

• The procedures are provided by Rickus lab group.