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From 2013.igem.org

Contents 1 Measuring the concentrations of isolated P. putida DNA from the previous day 2 Preparing samples to run on 1% gel 3 Running gel of P. putida DNA and Herring sperm DNA 4 Running sonicated herring sperm DNA on 0.8% gel

Measuring the concentrations of isolated P. putida DNA from the previous day

• Measuring concentration using nanodrop
• Blanking against buffer

Sample nr.	Concentration ng/ul	260/280	260/230
2	44	1.8	1.15
4	30.6	1.8	1.29
6	42.3	1.81	1.05
8	35.6	1.85	1.26
10	38.2	1.84	1.28
12	40.6	1.83	1.45
14	39.9	1.88	1.47
16	18.5	1.17	0.67

Preparing samples to run on 1% gel

• 500ng of each of the isolated P. putida DNA sample is run on gel
• Volumes are adjusted to 20ul per well accordingly (includes DNA, sterile H2O and OG)
• 5ul of orange G dye is added to each sample
• 5ul of 1kb ladders are used
• For sheared DNA, dilutions were loaded
  • 1ul of DNA was diluted in 9ul of 1xTE buffer to make up 10x dilution
  • 1ul from 10x dilution was put in 9ul of 1xTE buffer to make up 100x dilution
• Dilutions were nanodropped and the concentration for 100 fold dilution was 121 ng/ul
• 200ng of herring sperm DNA was run on gel
• One lane was left for control, non-sheared DNA, also 100 fold dilution

Running gel of P. putida DNA and Herring sperm DNA

Samples in lanes goes as follows: 1 Kb ladder, 2, 4, 6, 8, 10, 12, 14, 16, 1 kb ladder, 100x dilution of sheared herring sperm DNA, control 100x diluted herring sperm DNA

Running sonicated herring sperm DNA on 0.8% gel

• 3 lanes for running:
  • Sheared and sonicated
  • Unsheared and sonicated
  • Unsheared and unsonicated
• 5ul of 1kb marker is used
• The DNA samples are diluted 100 fold and 200ng of sample is run.
• Volume of sterile water is adjusted appropriately to make up 20ul of sample per well, including 5ul of orange G dye