How to Convert Primer Amounts and Concentrations: From nmol to µM (and µg/mL to µM)
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When you order primers for PCR, qPCR, or cloning, the company doesn’t usually ship you a solution. Instead, they send you a dried pellet containing a specific amount of DNA oligonucleotide (nmol or µmol). To use your primers, you’ll need to resuspend them into a stock solution of a known concentration (commonly 100 µM).
However, in the instance where you want to QC your primers, a spectrophotometer such as a NanoDrop, would be used. This QC instrument reports the primer concentration in ng/µL (same as µg/mL). To make sense of that number, you need to convert back into µM.
This post will walk you through both perspectives:
Starting with the shipped amount (nmol → µM).
If you QC with a NanoDrop (µg/mL → µM).
Part 1: From Shipped nmol to µM
Step 1: Check the datasheet
When you receive primers, the datasheet will tell you the total amount — for example: 30 nmol of primer.
Step 2: Choose your resuspension volume
To make a 100 µM stock solution (a standard working concentration):
Volume (µL) = Amount (nmol) / Desired concentration (µM)
Example:
Amount shipped = 30 nmol
Desired stock = 100 µM
Volume = 0.3 mL/100 = 0.3mL = 300µL
So, dissolve your 30 nmol primer pellet in 300 µL water/TE → 100 µM stock solution.
This approach is simple and is what most labs do.
Part 2: Checking by NanoDrop (Optional QC)
If you measure your resuspended primer on a NanoDrop, the output is usually given as ng/µL (which is equivalent to µg/mL).
Example NanoDrop readout: 660 ng/µL = 660 µg/mL.
To convert this into µM, you use the primer’s molecular weight (MW).
Step 1: Calculate primer MW
Rough rule: ~330 g/mol per nucleotide.
For a 20-base primer: MW ≈ 20 × 330 = 6600 g/mol.
Step 2: Conversion formula
Concentration (µM) = Concentration (µg/mL) × 1000 / MW (g/mol)
Worked Example
NanoDrop reading = 660 µg/mL
MW = 6600 g/mol
µM = 660×1000 / 6600 = 100µMµM
This confirms that the primer solution you prepared (30 nmol in 300 µL) is indeed 100 µM.
Expert QC Tip: Getting an Accurate μg/mL Reading
While the MW conversion confirms your concentration after the measurement, the most accurate QC requires you to ensure the NanoDrop's initial μg/mL number is correct.
Avoid the Default Factor: The NanoDrop often defaults to 33 ng−cm/μL (the general ssDNA factor). For short primers, this is inaccurate because the concentration factor is highly dependent on the oligo's specific sequence (e.g., how many Gs and Cs it has).
Use the Extinction Coefficient (ε): For true accuracy, you need to use the primer's unique molar extinction coefficient (ε) provided on the manufacturer's Certificate of Analysis.
Correct the NanoDrop Software: Before you measure, choose the "Oligo DNA" or "Custom Factor" application on the NanoDrop and input your specific ε value. This tells the machine the correct A260 to μg/mL conversion, making your initial reading trustworthy.
The MW helps you convert μg/mL to μM; the ε helps the NanoDrop accurately determine the initial μg/mL reading in the first place. Use both for a proper QC!
Other Measures of Purity Ratios
You might notice the NanoDrop reports the A260/A280 and A260/A230 ratios (the standard purity checks for longer DNA). For short oligonucleotides, these ratios are often unreliable! Because primers are so short, the shape of their UV spectrum is highly dependent on their sequence, meaning the classic "pure" values of 1.8 or 2.0 often don't apply. While the ratios are still useful for checking gross contamination, don't worry if your primer's ratios look unusual—focus on the concentration!
Why You Need To Know Both Types of Calculations
Shipped nmol → µM: Use this for preparing stocks straight from the primer tube.
NanoDrop µg/mL → µM: Useful as a double-check or when you want to report DNA concentrations after QC.
Both methods arrive at the same place — the NanoDrop just gives you a way to verify.
References
Thermo Fisher Scientific. (2014). Accurate Oligonucleotide Quantification with NanoDrop Spectrophotometers(Application Note 52607). https://assets.thermofisher.com/TFS-Assets/CAD/Application-Notes/TN52607-E-0914M-Oligonucleotides-Mweb.pdf
Sigma-Aldrich. (n.d.). Oligonucleotide Handling & Stability. Retrieved October 6, 2025, from https://www.sigmaaldrich.com/US/en/technical-documents/protocol/genomics/dna-and-rna-purification/oligonucleotide-handling-and-stability
Desjardins, P., & Conklin, D. (2010). NanoDrop microvolume quantitation of nucleic acids. Methods in Molecular Biology (Clifton, N.J.), 616, 29–42. https://doi.org/10.1007/978-1-60327-414-2_
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