License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: November 06, 2023
Last Modified: November 20, 2023
Protocol Integer ID: 90475
Keywords: Nanodrop, DNA purity, A260/280, Spectrophotometer
Funders Acknowledgement:
National Institute for Health and care Research
Grant ID: 16/136/111
Disclaimer
This protocol has been adapted from nucleic acid purity measurement assays developed by ThermoFisher Scientific.
Abstract
A standard technique for performing purity measurements is UV absorbance with a spectrophotometer. Microvolume spectrophotometers are commonly used for the analysis of nucleic acid samples. They require a small sample volume (0.5–5.0 μl) and are economical, convenient and widely available. Typically, they measure concentration and purity readings for ssDNA, dsDNA and RNA and can provide meaningful insights into the quality of the sample.
Due to some reported limitations with this method, we would recommend deploying Nanodrop UV spectrophotometry ONLY for purity ratio estimations (A260/280 and A260/230) of double-stranded or single-stranded DNA/RNA, especially when destined for downstream applications such as DNA library preparation for whole-genome, amplicon and targeted sequencing.
As an indicator of sample purity, the ratios of the absorbance values at 260 nm vs 280 nm (A260/A280) and at 260 nm vs 230 nm (A260/A230) need to be determined for each sample to ensure its suitability for downstream applications. The A260/A280 provides insight into the type of nucleic acid present (dsDNA or RNA) as well as an indication of purity. Typically, protein contamination can be detected by a reduction in this ratio; RNA contamination can be detected by an increase in this ratio. In buffered solutions, pure dsDNA has an A260/ A280 of 1.85–1.88.
The A260/A230 is a sensitive indicator of contaminants that absorb at 230 nm. These contaminants are significantly more numerous than those absorbing at 280 nm, and include chaotropic salts such as guanidine thiocyanate (GTC) and guanidine hydrochloride (GuHCl), EDTA, non-ionic detergents like Triton™ X-100 and Tween® 20, proteins, and phenol. Substances like polysaccharides or free floating solid particles like silica fibers absorb at this wavelength, but will have a weaker effect. In buffered solutions, pure dsDNA has a higher A260/A230 ratios at 2.3–2.4. A260/A230 ratios typically produce a higher standard deviation than A260/ A280 ratios and should be interpreted with care.
This protocol has been adapted from nucleic acid purity measurement assays developed by ThermoFisher Scientific.
3. Kimberly-Clark™ Professional Kimwipes™ Delicate Task Wipers (Cat no. 33670-04)
4. Nuclease-free Water (Local supplier)
5. Elution buffer stock (used to dissolved the DNA during extraction)
6. Calibrated single- or multichannel pipettes (P2 and P10) with compatible sterile, low-retention, filtered tips.
Optional:
7. 0.1M hydrochloric acid solution
Before Starting
Before Starting
2m
2m
An initial cleaning of measurement surfaces with nuclease-free (NF) water is recommended prior to making the blank measurement.
To clean the pedestal, pipette 2 µL of NF water onto the pedestal and lower the arm. Leave to sit for 00:01:00 and then wipe away with lint-free tissue.
Fig. 1a and 1b illustrate the loading technique and how the droplet sits on the pedestal.
A final cleaning of both measurement surfaces with nuclease-free (NF) water is also recommended after the last sample measurement.
1m
Prior to initiating the protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared for DNA quantification according to local GLP guidelines.
Create an organised bench space by clearing away all clutter in order to maximize work efficiency.
Initialisation
Initialisation
Open up the Nanodrop software from the desktop shortcut. Choose the type of sample to be measured (in this case, Nucleic Acid , then dsDNA)
At the prompt, pipette 2 µL of NF water onto the pedestal and click OK. This will complete initialisation of the Nanodrop instrument.
Blank Measurement
Blank Measurement
Once again, select the type of sample that needs to be measured. Load 2 µL of the blanking buffer onto the lower measurement pedestal and lower the sampling arm.
Click Blank to measure and store the reference spectrum.
After the measurement is complete, use a dry, lint-free lab wipe to remove the buffer from both the top and bottom measurement surfaces (Fig. 2).
Pipette another 2 µL of the blanking buffer onto the pedestal, lower the arm and click Measure. The result should be a spectrum that varies no more than 0.04 Abs (10 mm absorbance equivalent) from the baseline at 260 nm. If not, clean the measurement surfaces and repeat steps 1-5.
Sample Measurement
Sample Measurement
After the blank measurement is complete, enter the sample name in the Sample ID box, and choose the appropriate sample type as indicated below in Table 1:
Pipette 2 µL of the gDNA sample onto the lower measurement pedestal and lower the sampling arm. Click Measure.
After the measurement is complete, use a dry, lint-free lab wipe to remove the buffer from both the top and bottom measurement surfaces (Fig. 2).
Review spectral image to assess sample quality (Fig. 3).