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Star Republic: Guide for Biologists

Oligonucleotide mole/weight/concentration calculations

1. Calculate the extinction coefficient (e) for the oligonucleotide.

e260 ~ 0.89 * ( #A * 15,480 + #C * 7,340 + #G * 11,760 + #T * 8,850 ) (M-1 cm-1)
or use the average e260 ~ 9700.

2. Dissolve the oligo in a small volume of TE or H2O. Take a small aliquot of the oligo, add to 1 ml of H2O, and measure OD at A260. Dilute if necessary so the OD reading will be in the range 0.1-1.

3. Calculate molecular weight for the oligo using BioToolKit or the following formula:

Molecular weight (Dalton) = 313.21 * Number of A + 289.18 * Number of C + 329.21 * Number of G + 304.21 * Number of T - 61

On average, Molecular weight ~ 309 * length - 61.

4. Correction for sodium and ammonium salts. Add 22 * length for sodium salt or 17 * length for ammonium salt.

5. To calculate concentration (weight/volume), use the following:

Concentration ( mg/ml ) = A260 * 103 * (Molecular Weight) / e260

or use the approximation

Concentration ( mg/ml ) ~ A260 * 30

6. For molar concentration,

Molar concentration (nM, picomoles/ml) = A260 * 109 * (Molecular Weight) / e260
or use the approximation Molar concentration (nM, picomoles/ml) ~ A260 * 106.

7. Multiply total fold of dilution to obtain the concentration for your stock solution. If you take 1 ml from your oligo stock and add to 1 ml of H2O for OD measurement, the total fold of dilution will be 1000.

8. Adjust the volume of your stock solution with TE or H2O to obtain the desired molar or weight concentration.