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From 2010.igem.org

Contents 1 Aim of this experiment 2 Materials and methods 3 Gram-positive Bacteria Chromosomal DNA Extraction Protocol 3.1 Puregene DNA isolation 3.2 Cell Lysis 3.3 RNase Treatment 3.4 Protein Precipitation 3.5 DNA Precipitation 3.6 DNA Hydration 4 Results 5 Conclusion

Aim of this experiment

The aim of this experiment was to extract genomic DNA from Bacillus subtilis strain ATCC 6633. This strain produces the subtilin genes, required for our Quorum Sensing BioBrick.

Materials and methods

• ara forward and reverse primers
• spac forward and reverse primers
• Pipettes
• Universal tubes
• Eppendorf tubes
• Centrifuge
• PCR
• Gel electrophoresis

ara and spac are two genes that exist in the ATCC 6633 strain. ara and spac forward and reverse primers are two tests, which will be used in PCR. At the end, Gel Electrophersis can be used to distinguish th bands. If the bands from either of ara or spac show up at the expected bps against the DNA ladder, this proves that the genomic DNA is sucessfully extracted.

Gram-positive Bacteria Chromosomal DNA Extraction Protocol

Puregene DNA isolation

1. Grow overnight 7.5ml cultures in THYB containing 30μg/ml hyaluronidase.

Cell Lysis

1. Two sets of chromosomal DNA were being done.
2. Cells go through 3600 x g centrifugation for 15 minutes to pellet.
3. The supernatant in the tubes are poured away.
4. 0.5ml of cell suspension solution is added to the eppendorf tubes. The solution in the tubes are pipetted up and down to resuspend cells. The solution is then transferred to another 1.5ml tube.
5. 50μl of lysozyme and 7.5μl of lytic enzyme solution is added into each tube. The tubes are then inverted 25 times to mix the solution.
6. We then incubate them at 37°C for 30 minutes in order to digest the cell walls. The tubes are inverted occasionally during incubation.
7. To pellet the cells, we centrifuged it for 10 minutes and poured away the supernatant after that.
8. 0.5ml of cell lysis solution is added to the pelleted cells and the solution is pipetted up and down in order to lyse the cells. The samples are then heated for about 5 minutes at 80°C.

RNase Treatment

1. 6μl of RNase A solution is added into the cell lysate.
2. The tubes are inverted 25 times in order to allow the solutions to mix. They are then incubated at 60minutes at 37°C.

Protein Precipitation

1. The samples are cooled on ice.
2. 0.5ml of protein precipitation solution is added into each tube.
3. The solutions are vortexed at high speed for about 20 seconds for the protein precipitation solution to mix properly with the cell lysate. The samples are then placed on ice for 5 minutes.
4. They are then centrifuged at 13000rpm for 1 minute for the proteins to form a tight pellet.

DNA Precipitation

1. The supernatant containing the DNA are poured into a clean eppendorf tube.
2. 0.5ml of isopropanol is then added into each tube.
3. The solutions are then mixed by inverting gently for 50 times.
4. The mixture is centrifuged at 13000rpm for 1 minute. The DNA can be seen as a small white pellet at the bottom of the tubes.
5. The supernatant is poured off and the tubes are drained on a clean absorbent paper. 0.5ml of 70% ethanol is added into the tubes and are inverted a few times to wash the DNA.
6. They are then centrifuged for 1 minute at 13000rpm. After that, ethanol is poured off leaving the DNA behind.
7. The tubes are drained on clean absorbent paper. They are allowed to air dry for 10-15 minutes.

DNA Hydration

1. 100μl of DNA hydration solution is added to each tube.
2. DNA is rehydrated by incubating the sample for one hour at 65°C and overnight at room temperature.

Results

Results were as expected see: https://2010.igem.org/Team:Newcastle/7_July_2010

Conclusion

See: https://2010.igem.org/Team:Newcastle/7_July_2010