Luckau Protocols:NanoDrop
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NanoDrop Protocol |
Purpose
The NanoDrop is used to quantify genetic material. Although there are many different methods to quantifying DNA, the NanoDrop is a spectrophotometer that calculates absorbance of a sample across different wavelengths.
Protocol
- Assemble cafeteria tray
- Kim Wipes
- 2µL pipette
- pipette tips
- gloves
- USB drive
- water and buffer tubes
- samples
- The NanoDrop is located in North Life Sciences, room 325A
- Open the NanoDrop software, "ND1000" on the desktop
- Choose "Nucleic Acids"
- Initialize the instrument
- ensure upper and lower pedestal surfaces are clean by wiping with Kim Wipe
- Place 2µL of NanoPure water on the lower pedestal
- Lower the sampling arm and press OK
- when it's done, wipe upper and lower pedestals with Kim Wipe
- Calibrate the instrument
- Place 2µL of elution buffer on the pedestal
- For Clark's lab, elution buffer is 10mM Tris-Cl, pH 8.4
- Click "Blank"
- when it's done, wipe upper and lower pedestals with Kim Wipe
- Measure sample
- Place 2µL of sample on the pedestal
- Enter sample ID
- Click "Measure"
- wipe upper and lower pedestals with Kim Wipe after each sample
- Re-calibrate the instrument each 10 samples, or so, by going back to step 6 and clicking "Re-Blank" instead of "Blank"
- Save data
- Click "Show Report"
- Click "Reports", "Save Report"
- Click "Export Report Table Only"
- save to your USB drive, as "YYYYMMDD_NanoDrop", use "A" "B" "C", etc to designate multiple saved files in the same day
- Re-initialize the instrument each 30-50 samples, by going back to step 3
- remember to save your data before your re-initialize
- Clean up thoroughly! Other people use this instrument!
- don't forget to enter data into spreadsheet
Purity Assessment
- ratio of sample absorbance at 230, 260 and 280nm is used to assess sample purity. The ratios and information relevant to our work with DNA is given below:
260/280 Ratio
- used to assess purity of DNA and RNA
- pure DNA: ~1.8
- <1.8 → residual reagent form extraction, low nucleic acid concentration (<10 ng/µL)
- >1.8 → not an issue!
260/230 Ratio
- used as a secondary measure of nucleic acid purity
- pure nucleic acid: 2.0-2.2
- <2.0 → residual guanidine
- >2.2 → blanked on dirty pedestal, inappropriate blank (should be same pH and ionic strength)