Protocols

[1A] Polymerase Chain Reaction

PCR is used to rapidly amplify certain segments of DNA that are selected via designed primers. This protocol was used to accomplish a variety of goals, from extraction of parts from a cloning vector to the addition of restriction cut sites at the ends of parts.

1. Defrost template, 2x Master Mix and primers
2. Determine desired total working volume (~25uL)
3. Label reaction tubes
4. Create below reaction mix
5. Place mixture in thermal cycler at settings shown below

Sample Reaction

This is an example protocol used in the thermal cycler, durations and temperatures subject to change

[1B] PCR Cleanup

The Qiagen Qiaquick PCR cleanup kit was used to purify the thermal cycler product and remove remaining polymerases and nucleotides.

1. Gather the solutions from the PCR cleanup kit
2. Mix 5 times volume of Buffer PB with PCR reaction tube
3. Add 10uL 3M sodium acetate
4. Spin down the mixture in a QIAquick filter column at max speed for 60s. Discard flow-through and replace column into tube
5. Add 750uL of Buffer PE to the mixture and spin down at max speed for 60s to wash. Discard flow-through and replace column
6. Centrifuge the tube one more time to remove any remaining wash buffer
7. Place column in clean 1.5mL plastic tube
8. Add 30uL of Buffer EB to the column and let stand for 1min. Centrifuge at max speed for 1 min.

[2A] DNA Restriction Digest

1. Gather DNA sample, digestion buffer, and restriction enzymes from cold storage
2. Label tubes
3. Create the below reaction mixture
4. Place mixture in 37°C heat block for 10 minutes

[2B] Gel Verification/Extraction

1. Make 1% gel by adding .6g of agarose to 60mL of 1x TAE buffer
2. Swirl in glass flask and microwave for 40s
3. Remove from microwave and swirl again. Microwave again for 40s
4. Let cool until safe to touch. Add 6uL of SYBR safe red stain
5. Pour mixture into gel mold with comb set up
6. Fill gel electrophoresis apparatus with 1x TAE
7. Remove comb from gel and submerge gel in apparatus
8. Add 4uL of 1kb+ blue ladder to the first well
9. Add samples mixed with loading dye to other wells
10. Connect negative/positive ends to apparatus. Run at 110V
11. Run for 30min-1hr. Remove and take to UV imager
12. Photograph under UV light. If doing gel extraction, use scalpel to cut out blocks of gel containing desired bands
13. Gel purify using Qiagen Gel Purification kit
14. (If extracting)Use Nanodrop Spectrophotometer to measure DNA concentration