Gate Anneals

Room Temperature Annealing

1. Mix gate and output in a 1.2:1 ratio in a tube.
2. Cover the tube in foil, if you didn't use an opaque/black tube.
3. Leave the tube on a bench top overnight.

Annealing With Heatblock

1. Preheat the heat block to 95°C, add water to the well you will be using.
2. Put a piece of styrofoam (covered with foil) on the heat block. Make sure the temperature is still at 95°C, and doesn't jump
3. Mix gate and output in a 1.2:1 ratio in a tube, put it in the heat block.
4. Cover again with the styrofoam, set the heat block to RT.
5. 5. Wait until the block cools. It will probably not reach RT, but will be at around 30°C after a few hours. Turn the block off completely and wait for a bit (1h).

 N.B. It may be possible to anneal using a lower maximum temperature (say, 80°C), as long as it is higher than the melting temperature of the oligos.

 *Adapted from Qian L, Winfree E. Scaling up digital circuit computation with DNA displacement cascades. , Science. 2011 Jun 3;332(6034):1196-201.

Plate Reader Studies

Kinetic Studies

1. Prepare wells: 100 µL 1X TAE, 12.5 mM Mg2+ buffer; 10 nM 100 µL RNA-ROX (gate); 10 nM 100 µL gate:output complex; 10 nM 100 µL gate:output complex.
2. Measure fluorescence of all wells for 1 minute (5 seconds between measurements).
3. Add 1 µL of the buffer to the buffer and gate wells. Add 1 µl of 1 µM input S6 to the first gate:output well; add 1 µL of 1 µM input S1 to the second gate:output well. Note: Mix well by pipetting into the well, after adding input shake the plate by doing a sort of swirling motion in a plane. If possible, set the plate reader to do this for you for 3 seconds with a 1 second rest time.
4. Measure fluorescence of all wells for 10 minutes (5 seconds between measurements).

 *Adapted from Qian L, Winfree E. Scaling up digital circuit computation with DNA displacement cascades. , Science. 2011 Jun 3;332(6034):1196-201.

DNA Transfection

1. Label enough eppendorf tubes for the number of conditions/wells you are transfecting plus one for a master mix of transfection reagent and unsupplemented DMEM. If possible, try to pool conditions/wells, i.e, if doing a small molecule induction ladder.
2. Aliquot 50 uL of unsupplemented DMEM to every tube. If you are pooling n conditions/wells, aliquot 50*n. For your mastermix, aliquot 50* total number of conditions/wells of unsupplemented DMEM.
3. Dilute plasmid DNA in tubes containing 50 (or 50*n) unsupplemented DMEM. Be sure to mix well. For our transfections, we transfect at most 500 ng of plasmid DNA. Be sure that DNA is of high purity and concentrated enough that it can be pipetted in small volumes (from .5 uL- 1 uL). Anything larger will dilute the final concentration.
4. Dilute transfection reagent into unsupplemented DMEM to create the mastermix. We use 1.65 uL Lipofectamine per 500 ng of plasmid DNA per well. So, if transfecting n conditions/wells, dilute 1.65 * n transfection reagent.
5. Add 51.65 uL of master mix per tube and pipette gently to mix. If pooling, mix 51.65 * # of conditions pooled. Let complexes form for 20 minutes in the hood.
6. While complexes are forming, cells must be seeded into a 24 well plate at 100,000 cells in 500 uL. Note. If transfecting in glass bottom well plates, you must pretreat with gelatin (see menu).
7. Trypsinize and count confluent cells. Centrifuge at 1180 rpm for 4 minutes and resuspend in fresh media. Dilute to the 100,000 cells/ 500 uL. Add 500 uL of cells to each well.
8. When complexes are done forming, add dropwise to each well. Swirl the entire plate to mix, and then place into an incubator. Small molecule induction can be done 24 hrs later, and gene expression can be assayed 48 hrs later.

 *Adapted from Invitrogen, Lipofectaime® 2000 Reagent Product Manual.

RNA Transfection

1. Label enough eppendorf tubes for the number of conditions/wells you are transfecting plus one for a master mix of transfection reagent and unsupplemented DMEM. If possible, try to pool conditions/wells, i.e, if doing a small molecule induction ladder.
2. Aliquot 50 uL of unsupplemented DMEM to every tube. If you are pooling n conditions/wells, aliquot 50*n. For your mastermix, aliquot 50* total number of conditions/wells of unsupplemented DMEM.
3. Dilute RNA in tubes containing 50 (or 50*n) unsupplemented DMEM. Be sure to mix well. Be sure that RNA is concentrated enough that it can be pipetted in small volumes (from .5 uL- 1 uL). Anything larger will dilute the final concentration. (insert something here about separate vesicle formation for inputs, G:O etc.

 *Adapted from Invitrogen, Transfecting Stealth™ or siRNA into Mammalian Cells using Lipofectamine™ RNAiMAX.

DNA and RNA Cotransfection

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Gelatin Pretreatment

This protocol is for use in 24 well plate format. It can be scaled up or down depending on what size dish you are using.

1. Pipette x uL of .1 (w/v) % sterile, ultrapure gelatin into each well.
2. Let the well plate incubate for at least 20 mins before aspirating off the gelatin.
3. Plates can then be used for transfection, in particular those that will be used for microscopy.

Passaging Cells

Note. This protocol is for culturing cells in 100mm^2 round dishes. For other culture volumes, the amounts of reagents required will be different. Before moving cells from the incubator into the hood,

1. Wipe down hood with 70% EtOH.
2. Pre-warm reagents in a 37 °C water bath. For a full 500 mL bottle of media this can take up to 20 mins to fully warm.
3. Anything moving into the hood, especially from the water bath, must be washed off with 70% EtOH.

Once your hood and reagents are ready,

1. Move cells from incubator to hood.
2. Aspirate off media using a sterilized (autoclaved), glass pastuer pipette, or a disposable aspirating pipette.
3. Optional: Wash cells gently using 2.5 mL PBS, then aspirate.
4. Add 2.5 mL of trypsin to cells. Incubate at most 1 min at 37°C. Work quickly, as over trypsinization will damage the cells.
5. Add 9.5 mL of supplemented media to inactivate trypsin. Pipette to get cells into a single cell suspension.
6. Pipette cells into a conical tube and take note of the final volume (which should be 12mL). This will dictate how much is transferred to a new cell culture dish. If splitting 1:6, then you need 2 mL of cell solution.
7. After transferring cells to new culture dishes, add supplemented media to a final volume of 12-13 mL.
8. Label dishes with Name, Date, Cell type, splitting ratio, and passage number.
9. Place cells into incubator.
10. Destroy unused cells by aspirating into the vacuum trap, or by adding bleach.
11. Wash out of hood with 70% EtOH, close the sash, and turn on UV Light.

Preparing Samples for Flow Cytometry

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