Reactants

Thermocycler (Ross Phusion)

Reactants

Reactants w/o Mastermix

Thermocycler (Touchdown)

1. 100 mL TAE buffer + 1 g agarose (Nuseive 3:1)
2. Stir
3. Microwave
4. Add 1 drop of EtBr
5. Use large combs for 50 uL PCR reactions and small combs for 10 uL reactions
6. Let the gel cool

1 kb ladder (2 µL), loading dye (2 µL), water (8 µL)
pcr product (45 µL), dye (7.5 µL) (6:1 ratio)

1. Load and run the dye
2. Weight a 1.5 mL microcentrifuge tube for each DNA fragment to be isolated and record weight.
3. Visualize and photograph the DNA using a long-wavelength UV lamp and an intercalating dye (EtBr). Excise DNA fragment of interest in a minimal volume of agarose using a clean scalpel or razor blade. Transfer the gel slice to the weighed microcentrifuge tube and record the weight. Subtract the weight of the empty tube from the total weight to obtain the weight of the gel slice. The gel slice may be stored at 4°C or at –20°C for up to one week in a tightly closed tube under nuclease-free conditions before purification.

   Notes: The gel slice may be stored at 4°C or at –20°C for up to one week in a tightly closed tube under nuclease-free conditions before purification.

4. Add Membrane Binding Solution at a ratio of 1 mL of solution per 1 g of agarose gel slice.
5. Vortex the mixture and incubate at 50–65°C for 10 minutes or until the gel slice is completely dissolved. Vortex the tube every few minutes to increase the rate of agarose gel melting. Centrifuge the tube briefly at room temperature to ensure the contents are at the bottom of the tube. Once the agarose gel is melted, the gel will not resolidify at room temperature.

1. Place one SV Minicolumn in a Collection Tube for each dissolved gel slice or PCR amplification.
2. Transfer the dissolved gel mixture or prepared PCR product to the SV Minicolumn assembly and incubate for 1 minute at room temperature.
3. Centrifuge for 1 minute and discard liquid.
4. Wash with 700 µl of Membrane Wash Solution, centrifuge 1 minute, and discard.
5. Wash with 500 µl of Membrane Wash Solution, centrifuge 5 minutes, and discard.
6. Centrifuge 1 minute with the microcentrifuge lid open (or off ) to allow evaporation of any residual ethanol.
7. Transfer SV Minicolumn to a clean 1.5 ml microcentrifuge tube.
8. Apply 15 µl of Nuclease-Free Water directly to the center of the column. Make sure membrane is completely covered with Nuclease-free water. Incubate at room temperature for 1 minute. Centrifuge 1 minute at 16,000 × g. Repeat.
9. Discard SV Minicolumn, store tube containing the eluted DNA at 4°C or –20°C.

Notes for "DNA Purification by Centrifugation":

1. MWS = Membrane Wash Solution
2. RT = room temperature
3. Centrifuge at 16,000 x g

Nanodrop/Speed Vac: if concentration not high enough, speed vac and measure again.

Protocol:All centrifugation steps should be performed between 10,000 - 16,000 x g

1. In a 1.5 ml microcentrifuge tube, add 2-7 volumes of DNA Binding Buffer to each volume of DNA sample (see table below). Mix briefly by vortexing.

Application	DNA Binding Buffer: Sample	Example
Genomic DNA (>2 kb)	2 : 1	200 uL : 100 uL
PCR Product DNA Fragment	5 : 1	500 uL : 100 uL
ssDNA (eg. cDNA, M13 Phage)	7 : 1	700 uL : 100 uL

2. Transfer mixture to a provided Zymo-Spin™ Column in a Collection Tube.
3. Centrifuge for 30 seconds. Discard the flow-through.
4. Add 200 µl DNA Wash Buffer to the column. Centrifuge for 30 seconds. Repeat the wash step. 5. Add 7 uL water directly to the column matrix and incubate at room temperature for one minute. Transfer the column to a 1.5 ml microcentrifuge tube and centrifuge for 30 seconds to elute the DNA.
5. Ultra-pure DNA is now ready for use.

Note: All centrifugation steps should be performed between 10,000 - 16,000 x g

Note:

• 10 ng/kb
• If <500 bp, add double or triple

Gibson Mix¹, 1.3 X 15 uL
Insert² (~20 ng/uL) 2.5 uL (50 ng)
Vector PCR 2.1³ 2.5 uL
Total Vol 20 uL

1. Incubate 1 hour at 50 C in thermocycler.

• 15 uL aliquots in pcr tube box OR box next to antibiotics in B lab freezer
• PCR product (gel purified or pcr clean-up’d)
• Blue sticker

1. Place Gibson reaction on ice.
2. Thaw on ice one 50 uL vial of One Shot TOP10 cells* for each ligation/transformation.
3. Pipette 5 uL of each Gibson reaction (OR 1 uL of miniprep) directly into the vial of competent cells and mix by tapping gently. Do not mix by pipetting up and down. The remaining Gibson mixture(s) can be stored at -20 C.
4. Incubate vials on ice for 30 minutes.
~take out vial of SOC~
5. Incubate for exactly 30 seconds in the 42C water bath. Do not mix or shake.
6. Remove vial(s) from 42C bath and place them on ice.
7. Add 250 uL of pre-warmed SOC medium to each vial. SOC is a rich medium; sterile technique must be practiced to avoid contamination.
8. Place vials in microcentrifuge rack on its side and secure with tape to avoid loss of the vial(s). Shake the vial(s) at 37 C for exactly 1 hour at 225 rpm in a shaking incubator.
~take out agar plates. place at 37 C~
9. Spin down and resuspend in 100 uL LB.
10. Spread 50 uL from each transformation vial on separate, labeled LB agar plates. Store the remaining transformation mix at 4C.
11. Invert the plates and incubate at 37 C overnight.
12. Select colonies and analyze by plasmid isolation, pcr or sequencing.
*B lab freezer, bottom row, right most, white pcr tube box.

1. Resuspend pelleted bacterial cells in 250 µl Buffer P1 (w/ RNase A*) and transfer to a microcentrifuge tube. No cell clumps should be visible after resuspension of the pellet.
2. Add 250 µl 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 µl 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.
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 DH5α™ do not require this additional wash step.
8. Wash QIAprep Spin Column by adding 0.75 ml Buffer PE and centrifuging for 30–60 s.
9. Discard flow-through; centrifuge 1 min to remove residual wash buffer.
10. Place the QIAprep column in a clean 1.5 ml microcentrifuge tube.
11. To elute DNA, add 25 µl 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. Repeat for 2x DNA.
*want 50 ug/mL RNase A in P1

use Hotstart taq PCR supermix (platinum) instead of Accuprime pfx
touchdown protocol for thermocycler

Reagents

Fresh PCR Product	0.5 - 4 µL
Salt Solution	1 µL
Water	Add to Final Volume 5 µL
Template	1 µL
TOPO Vector	1 µL
Volume Total	6 µL

1. Mix reaction gently and incubate for 5 minutes at room temperature (22-23°C).
Note: For most applications, 5 minutes will yield plenty of colonies for analysis. Depending on your needs, the length of the TOPO® Cloning reaction can be varied from 30 seconds to 30 minutes. For routine subcloning of PCR products, 30 seconds may be sufficient. For large PCR products (> 1 kb) or if you are TOPO® Cloning a pool of PCR products, increasing the reaction time will yield more colonies.
2. Place reaction on ice.
Note: You may store the TOPO® Cloning reaction at -20°C overnight.

Continue to 5. Transforming TOP10 Competent cells

1. COWg 1, F and R
2. COWg 2, F and R
3. COWg 3, F and R
4. COWg 4, F and R
5. pET21, F and R