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Quantifying DNA with the NanoDrop

Created by Ravishankar Madhu

Last updated: 2023-07-10

Description

This protocol describes how to quantify DNA using the NanoDrop located in the Main Lab Space. While this measurement is accurate enough for the vast majority of labwork, some extremely delicate procedures (such as single cell sequencing) require the use of a more comprehensive quantification process (ie the Qubit)

Reagents and Materials

  • Extracted DNA (genomic or plasmid)
  • The Buffer the DNA is eluted in
  • DI-H20
  • NanoDrop Machine

Things to Note before starting

Troubleshooting

The computer attached to the NanoDrop is extremely old. Please be patient with the machine as it can take some time to load up. If there is issues with the computer recognizing the NanoDrop, try unplugging and replugging the NanoDrop.

Estimated Timing

The NanoDrop can quantify 8 samples of DNA at once. Running one round of quantification takes ~3-5 minutes.

Procedure

  1. Turn on the computer and log in.
  2. Double Click the NanoDrop Software (ND 8000).
  3. Click on Nucleic Acid. 1
  4. Add 5uL of DI-H20 to each sample well.
  5. Close the lid and confirm the dialog box that says to add water to each well to initialize the machine.
  6. Another dialog box will appear to tell you to blank the channels.
  7. Open the lid and wipe of all the channels with a Kimwipe.
  8. Add 3uL of the same buffer the DNA sample is in to each channel.
  9. Close the lid and confirm the dialog box telling you to blank the channels.
  10. Another dialog box will appear asking you to name the samples. Press X to close this dialog box.
  11. Open the lid and wipe of all the channels with a Kimwipe.
  12. Add 3uL of extracted DNA to the corresponding channel.
  13. Close the lid and press the Measure button in the upper left corner of the software.
  14. After a minute, the concentration should display on the right side of the software in ng/uL.
  15. Record the concentrations.
  16. Open the lid and wipe all of the channels with a Kimwipe.
  17. Add 5uL of DI-H20 to each channel.
  18. Close the lid and turn off the software.
  19. Log off of the machine.

Next Steps

Knowing the concentration of genomic DNA or plasmid is useful to run a PCR or a Virus Prep.

Appendix

Footnotes

  1. Even if you are trying to quantify a plasmid, always press the Nucleic Acid Button. ↩