Agarose Gel Electrophoresis of PCR products
DNA is uniformly negatively charged and will,therefore, move toward the positive electrode. The separation is determined by the size or mass of the molecule or fragments of DNA.
You will run your cleaned-up pcr products on a gel of 1.0 to 1.2% SeakemLE agarose solution (w/v) in 0.5x TBE buffer with Sybr Green stain to assess your success at amplifying 16s rDNA from each of your soil bacteria that you want to identify.
RUNNING THE GEL
Keep your pcr products on ice until your instructor tells you that the gel is ready to load.
1. Pipet 1μL of loading dye for each of your pcr products on a piece of parafilm (use a P10 and space out the drops so they are not near each other). You should have 5 pcr products per person: 4 bacteria to id and one neg (water) control.
2. Using a new tip, pipet 5μL of a pcr product into one of the drops of loading dye, mix with the pipet tip and then draw up all of it and dispense it into a well of the gel.
3. Fill out the gel template which identifies which bacterial strain is in each well.(Use a unique code name such as TR-1 --Tues.lab Red group- strain 1.) Make a copy of the template in your lab notebook.
4. Your instructor will add the ladder marker and a positive control and start the current when all students have loaded their samples.
5. When the gel has finished (usually 45 min. at 100volts), your instructor will photograph it under UV light, label the lanes from the template, and post the photo to the data folder on the conference.
How will you judge a successful amplification? How many fragments and of what size do you expect to see? Remember that you used the same "universal" bacteria primer pairs that we used in our other amplification of 16s rDNA from the genomic soil DNA extract but you used a less "picky" DNA polymerase, Taq, rather than an expensive proof-reading polymerase.
We will clean up all the successful amplifications.
Culturable Bacteria Identification continued
Read last weeks tests, Continue with new tests
Enterotube? Antibiotic sensitivity etc
set up nitogen recycling tests
add other "role" tests
Links to Labs