IGEM:The Citadel/Training

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=May Crash Course in Synthetic Biology=

In order to get some serious training under our belt, do something that helps iGEM, and start work that can be credited towards our project we will be testing Biobrick promoter strength on May 28-June 4th.

Those performing the training, make sure that you are familiar with "Measuring the activity of Biobrick Promoters Using an In vivo Reference Standard" by Jason Kelly et al.. The supplementary materials can be safely downloaded by clicking on| this link here. For a graphical summary of the protocol, travel over to the Parts Registry Measurement Section.


 * Note that we WILL NOT be doing Step #1 (synthesis and annealing of oligos to make a test promoter). Instead, we will be testing promoters that have been included with our distribution.

=COMPLETE PROTOCOL=

Materials
Equipment Chemicals and Reagents Supplies
 * -80&deg;C freezer
 * 37&deg;C incubator
 * Refrigerated centrifuge that accepts 225 mL culture tubes
 * ~500 mL LB Lennox supplemented with appropriate concentration of antibiotic if appropriate.
 * ~600 mL sterile deionized water chilled to 4&deg;C
 * 50 mL sterile 10% glycerol in deionized water chilled to 4&deg;C
 * Ice bucket and ice
 * Dry ice, ethanol bath
 * Many 1.5 mL plastic tubes chilled to -80 &deg;C
 * 14 mL culture tube for starter culture
 * 2 L flask for culture
 * 225 mL plastic tubes for centrifugation
 * Pipets

Procedure

 * 1) Prechill all tubes and pipets at 4&deg;C or -80&deg;C as appropriate. Also rinse all flasks with H2O prior to autoclaving in order to remove residual detergents that may remain on glassware from dishwashing.  This step may increase competency.  Autoclaving with water, which is then discarded, is even better.
 * 2) Inoculate 5mL LB medium and grow overnight at 37&deg;C with rotation. Use LB Lennox rather than LB Miller in order to lessen salt content of media
 * 3) Add the 5mL overnight culture to 450mL LB medium and incubate at 37&deg;C with vigorous shaking until the OD 600nm is between 0.5 and 1.0.  It should take about 3 hours. For recA- strains, the OD 600 nm should be between 0.5 and 0.7 according to one online source.
 * 4) Fast cool the centrifuge with the correct rotor to 4°C
 * 5) Pour the culture into two 225 mL centrifuge tubes.
 * 6) Place the tubes on ice for 15 minutes.  This step can vary in incubation time between 15 minutes and 1 hr.  Longer incubation times may lead to higher competency. For the following steps it is important to keep cells cold and remove all the supernatant in each step to remove residual ions.
 * 7) Centrifuge for 10 mins at 2000g at 4&deg;C
 * 8) Remove supernatant and gently resuspend pellets with 200mL cold sterile water.  Initially add 10-20 mL of water and resuspend by pipetting.  Then add the rest of the water.
 * 9) Centrifuge for 15 mins at 2000g at 4&deg;C
 * 10) Remove supernatant and gently resuspend pellets with 200mL cold sterile water.  Initially add 10-20 mL of water and resuspend by pipetting.  Then add the rest of the water.
 * 11) Hold on ice for 30 minutes
 * 12) Centrifuge for 15 mins at 2000g at 4&deg;C
 * 13) Remove supernatant and gently resuspend pellets with 25mL cold 10% glycerol.  This can be optionally transferred to a 50 mL conical tube.
 * 14) Hold on ice for 30 minutes
 * 15) Centrifuge for 15 mins at 1500g at 4&deg;C
 * 16) Remove the supernatant and add 500 &mu;l of 10% glycerol
 * 17) Resuspend the cells in a final volume of approximately 1 ml
 * 18) Aliquot 50 &mu;L per tube (tubes on ice)
 * 19) Shock freeze cell suspensions in a dry ice and ethanol bath.  One website recommended against using liquid nitrogen but did not justify this recommendation.
 * 20) Store at -80&deg;C

Materials
For the following, you need one per DNA sample
 * Electrocompetent cells
 * Plasmid DNA (from a ligation reaction)
 * Ice
 * Ice bucket
 * Electroporation cuvette (either 1mm or 2mm gap width)
 * Electroporator
 * 1.5 mL eppendorf tube
 * LB-agar plate with appropriate antibiotic
 * 1mL SOC at room-temperature

Procedure

 * 1) Chill electroporation cuvettes, DNA samples and tubes on ice.
 * 2) Place LB-agar plates in 37&deg;C incubator to warm.
 * 3) Once cuvettes are cold, remove electrocompetent cells from -80&deg;C freezer and thaw on ice. Alternatively, freshly prepared electrocompetent cells may be used immediately.
 * 4) If electrocompetent cells are not already in individual aliquots, then aliquot out into pre-chilled 0.6mL tubes.
 * 5) Turn on electroporator and set voltage to either 1.25 kV (1mm cuvettes) or 2.5 kV (2mm cuvettes).
 * 6) Dial a P2 pipetman to either 1 or 2&mu;L depending on the salt content of your DNA sample and . Use 2&mu;L for samples that have been purified in some way.
 * 7) Dial a P200 pipetman to 50&mu;L or whatever volume of electrocompetent cells you want to use. Usually 20-50&mu;L.
 * 8) Dial a P1000 pipetman to 950&mu;L and pipet in SOC. Place pipetman on counter such that tip doesn't touch anything.
 * 9) Pipet 1-2&mu;L of DNA sample and add to electrocompetent cells. Swirl tip around gently in cells to mix DNA and cells.  Do not pipet up and down.
 * 10) Place cells back on ice to ensure they remain cold.
 * 11) Transfer cell-DNA mixture to cuvettes using P200 pipetman. Try not to handle cuvette base too much so that it stays cold.
 * 12) Tap the cuvette on the counter gently so that cells are at the bottom and to remove any air bubbles.
 * 13) Wipe off excess moisture from outside of cuvette.
 * 14) Place in chamber of electroporator.
 * 15) Slide the chamber in so that the cuvette sits snugly between electrodes.
 * 16) Pulse the cells with a shock by pressing button on electroporator.
 * 17) Remove cuvette from the chamber and immediately add SOC. This step should be done as quickly as possible to prevent cells from dying off.
 * 18) Transfer SOC-cell mixture to chilled eppendorf tube.
 * 19) Chill sample on ice for 2 mins to permit the cells to recover.
 * 20) Transfer eppendorf tube to 37&deg;C incubator and shake to promote aeration. Incubate for 1 hr to permit expression of antibiotic resistance gene.
 * 21) Plate transformation onto prewarmed LB-agar plate supplemented with appropriate antibiotic. I generally plate 200&mu;L but appropriate plating volume depends on efficiency of the transformation.
 * 22) Incubate plate overnight at 37&deg;C.
 * 23) Leave remaining SOC-cell mixture on the benchtop overnight.
 * 24) If you don't have any transformants, plate the rest of the transformation in the morning.

Materials
For purifying plasmid DNA from Escherichia coli cells, the Qiagen Spin Miniprep Kit produces quite reliable results.

Do not autoclave solutions containing isopropanol or MOPS; use sterile filtration if necessary.

Buffer P1


 * 50 mM Tris-HCl pH 8.0
 * 10 mM EDTA
 * 100 &mu;g/ml RNaseA

The buffer and RNaseA can also be ordered from Qiagen separately (catalog numbers 19051 and 19101).

Buffer P2
 * 200 mM NaOH
 * 1% SDS

Buffer P3 (not for spin columns, but for Qiatips, midi, maxi, giga kits)
 * 3.0 M potassium acetate pH 5.5

Buffer N3
 * 4.2 M Gu-HCl
 * 0.9 M potassium acetate
 * pH 4.8

Buffer PB
 * 5 M Gu-HCl
 * 30% ethanol
 * (maybe add 10mM Tris-HCL PH 6.6, and that is better)

Buffer PE
 * 10 mM Tris-HCl pH 7.5
 * 80% ethanol

Buffer QBT equilibration buffer
 * 750 mM NaCl
 * 50 mM MOPS pH 7.0
 * 15% isopropanol
 * 0.15% triton X-100

Buffer QC wash buffer
 * 1.0M NaCl
 * 50 mM MOPS pH 7.0
 * 15% isopropanol

Buffer QF elution buffer
 * 1.25M NaCl
 * 50 mM Tris-HCl pH 8.5
 * 15% isopropanol

Buffer QN
 * 1.6M NaCl
 * 50 mM MOPS pH 7.0
 * 15% isopropanol

Buffer FWB2
 * 1M potassium acetate, pH 5.0

(Source:, [[media:US6383393.pdf | US Patent 6,383,393]])

The LyseBlue indicator dye added to some of the buffers is Thymophthalein, pH shift from colorless to blue at pH 9.3

Protocol
See here or here for the handbook for the Qiagen Spin Miniprep Kit. If you have never done this protocol before, read the the background information in the handbook (like the Important Notes section). It contains useful information. The following has been reproduced from the handbook and annotated based on experience with the kit.

Protocol: QIAprep Spin Miniprep Kit Using a Microcentrifuge

This protocol is designed for purification of up to 20 &mu;g of high-copy plasmid DNA from 1–5 ml overnight cultures of E. coli in LB (Luria-Bertani) medium. For purification of low-copy plasmids and cosmids, large plasmids (>10 kb), and DNA prepared using other methods, refer to the recommendations on page 37. Please read “Important Notes” on pages 19–21 before starting. Note: All protocol steps should be carried out at room temperature.

Procedure


 * 1) Resuspend pelleted bacterial cells in 250 µl Buffer P1 (kept at 4 &deg;C) and transfer to a microcentrifuge tube. Ensure that RNase A has been added to Buffer P1. No cell clumps should be visible after resuspension of the pellet.
 * 2) Add 250 &mu;l Buffer P2 and gently invert the tube 4–6 times to mix. Mix gently by inverting the tube. Do not vortex, as this will result in shearing of genomic DNA. If necessary, continue inverting the tube until the solution becomes viscous and slightly clear. Do not allow the lysis reaction to proceed for more than 5 min.
 * 3) Add 350 &mu;l Buffer N3 and invert the tube immediately but gently 4–6 times. To avoid localized precipitation, mix the solution gently but thoroughly, immediately after addition of Buffer N3. The solution should become cloudy.
 * 4) Centrifuge for 10 min at 13,000 rpm (~17,900 x g) in a table-top microcentrifuge. A compact white pellet will form.
 * 5) Apply the supernatants from step 4 to the QIAprep spin column by decanting or pipetting.
 * 6) Centrifuge for 30–60 s. Discard the flow-through. Spinning for 60 seconds produces good results.
 * 7) (Optional): Wash the QIAprep spin column by adding 0.5 ml Buffer PB and centrifuging for 30–60 s. Discard the flow-through. This step is necessary to remove trace nuclease activity when using endA+ strains such as the JM series, HB101 and its derivatives, or any wild-type strain, which have high levels of nuclease activity or high carbohydrate content. Host strains such as XL-1 Blue and DH5&alpha;™ do not require this additional wash step. Although they call this step optional, it does not really hurt your yield and you may think you are working with an endA- strain when in reality you are not. Again for this step, spinning for 60 seconds produces good results.
 * 8) Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifuging for 30–60 s. Spinning for 60 seconds produces good results.
 * 9) Discard the flow-through, and centrifuge for an additional 1 min to remove residual wash buffer. IMPORTANT: Residual wash buffer will not be completely removed unless the flow-through is discarded before this additional centrifugation. Residual ethanol from Buffer PE may inhibit subsequent enzymatic reactions. They are right about this.
 * 10) Place the QIAprep column in a clean 1.5 ml microcentrifuge tube. To elute DNA, add 50 &mu;l Buffer EB (10 mM Tris·Cl, pH 8.5) or water to the center of each QIAprep spin column, let stand for 1 min, and centrifuge for 1 min. If you are concerned about the concentration of the DNA, you can alternatively add 30 &mu;L water to the center of the column, incubate at room temperature on the bench for 5 mins and then centrifuge for 1 min. This will increase the concentration of DNA in your final sample which can be useful in some cases.  See notes below for why you should elute in water rather than the Buffer EB they recommend if you plan to sequence your sample.  Even if you are not sequencing, it may be beneficial to elute in water.  For instance, if you elute in buffer EB and you are using this DNA in a restriction digest, then the additional salts in your sample can affect the salt content of your digest.  This may matter with some finicky enzymes.

QIAGEN BUFFERS AND COLUMN RECYCLING
Clicking the link above will provide you with the compositions of the different buffers used by Qiagen, as well as instructions on how to conserve the column that are included with the kit.

NEB/GINKGO'S 3A BIOBRICK ASSEMBLY MANUAL
The above link redirects you to the protocol we will use for 3A standard assembly.

TK's RESTRICTION DIGEST
Materials
 * Restriction enzymes (EcoR I, Spe I, Xba I or Pst I) from NEB
 * NEB2 buffer
 * BSA
 * Deionized, sterile H2O

Digest Mix

''Example - 50 μL reaction. 100 μL reactions are also common especially if your DNA to be cut is dilute.''


 * 5 μL NEB2 buffer (for all digests with BioBricks enzymes, we use NEB2 buffer. It keeps things simple and seems to work).
 * X μL DNA (usually ~500 ng depending on downstream uses).
 * 0.5 μL 100X BSA (added to all digests because BSA never hurts a restriction digest)
 * 1 μL BioBricks enzyme 1 (regardless of the volume of the reaction, 1 μL enzyme is used because generally this represents a 10-25 fold excess of enzyme and is therefore sufficient for most digests. Also, it can be difficult to accurately pipet less than 1 μL of enzyme since it is sticky due to the glycerol content.)
 * 1 μL BioBricks enzyme 2
 * (42.5 - X) μL deionized, sterile H2O

Procedure 1. Add appropriate amount of deionized H2O to sterile 0.6 mL tube 2. Add restriction enzyme buffer to the tube. 3. Add BSA to the tube. 4. Add appropriate amount of DNA to be cut to the tube. 5. Add 1 μL of each enzyme. 6. Place in thermal cycler (MJ Research, PT-200) and run digest protocol. 7. Generally, use some method of DNA purification to eliminate enzymes and salt from the reaction.
 * Vortex buffer before pipetting to ensure that it is well-mixed.
 * Vortex BSA before pipetting to ensure that it is well-mixed.
 * Vortex DNA before pipetting to ensure that it is well-mixed.
 * Vortex enzyme before pipetting to ensure that it is well-mixed.
 * Also, the enzyme is in some percentage of glycerol which tends to stick to the sides of your tip. To ensure you add only 1 μL, just touch your tip to the surface of the liquid when pipetting.
 * 4-6 hour incubation at 37°C
 * Use a longer incubation time if you have time or are worried about the efficiency of cutting. I think this time can be shortened to 2 hrs while still cutting to completion.
 * 20 mins at 80°C to heat inactivate enzyme.
 * This step is sufficient to inactivate even Pst I.
 * 4°C forever (or until you pull the reaction out of the thermal cycler).

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