Daniel:Notebook/HiResChrPaint/2014-1-14
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Alu Control (Started 1/08/2014)[edit]
Dye Coupling Test (with Positive Control)[edit]
Repeating the dye coupling test one last time using a positive control as well.
- Following ARES Protocol
Samples
0. Vaccuum centrifuge DNA; resuspend in 6 uL nfH2O +3 uL sodium bicarbonate buffer 1. Warm DMSO and bicarbonate labeling buffer and nuclease free water to room temperature 2. Add 3 uL of sodium bicarbonate buffer 3. Dissolve 1 vial of reactive dye in 4 uL solvent; vortex ≥10 seconds *dye cannot be saved for later use. Use immediately! 4. Add 1 uL dye to each sample 5. Incubate in the dark for 1 hour 6. Add 20 uL nfH20 to sample; 7. Take 5 uL from sample and dilute with 45 uL nfH2O; Measure concentration in Nanodrop 8. Centri-Sep column purification 9. Measure concentration in Nanodrop
Labeling Results[edit]
Sample | ng/uL dsDNA | pmol/uL dye | pmol/uL ds probe | dye/100bp | ng/uL ssDNA | pmol/uL dye | pmol/uL ss probe | dye/100bp |
Alu2D-Pre Column | 170 | 115 | 113.2 | 116.6 | ||||
Blank-Pre Column | 157.4 | 111 | 103.3 | 110.6 | ||||
Cot1-Pre Column | 150.9 | 105 | 102.1 | 106.4 | ||||
V6S3-Pre Column | 160.3 | 109.2 | 109.6 | 112.9 | ||||
Alu2D-Post Column | 24.4 | 0.5 | 0.4 | 1.4 | 12.6 | 0.5 | 0.4 | 1.3 |
Blank-Post Column | 1 | 0 | 0.0 | 0.0 | 0.2 | 0 | 0.0 | 0.0 |
Cot1-Post Column | 25.9 | 1.7 | 0.2 | 4.3 | 15.6 | 1.3 | 0.3 | 2.8 |
V6S3-Post Column | 41.3 | 0.6 | 0.8 | 1.0 | 24.4 | 0.3 | 0.9 | 0.4 |
This is a big table, but there are a couple of messages to take away from this.
- Excess dye causes a false DNA reading. It doesn't appear to have an effect when dye concentration is low, but when the dye concentration was high (pre-spin column), even the blank sample measured a considerable amount of DNA. I'd recommend always using a blank column and subtracting the background from future samples if pre-purification measurements are needed.
- The Cot1 DNA is reproducibly eluting with dye. Given the other labeling results from previous days (1/13/2014 and 1/10/2014), I'd say that the Cot1 DNA, although having no amine groups, might be being labeled anyway. Or, at least, it's clogging up the column and allowing the dye to co-elute.