1. Calculate the extinction coefficient (e)
for the oligonucleotide.
e_{260} ~
0.89 * ( #A * 15,480 + #C * 7,340
+ #G * 11,760 + #T * 8,850 ) (M^{1}
cm^{1})
or use the average e_{260} ~ 9700.
2. Dissolve the oligo in a small volume of TE or H_{2}O.
Take a small aliquot of the oligo, add to 1 ml of H_{2}O, and measure OD at A_{260}.
Dilute if necessary so the OD reading will be in the range 0.11.
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 ) = A_{260} * 10^{3} * (Molecular Weight) / e_{260}
or use the approximation
Concentration ( mg/ml ) ~ A_{260} * 30
6. For molar concentration,
Molar concentration (nM, picomoles/ml) = A_{260} * 10^{9} * (Molecular Weight) / e_{260}
or use the approximation Molar concentration (nM, picomoles/ml) ~ A_{260} * 10^{6}.
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 H_{2}O for OD measurement, the total
fold of dilution will be 1000.
8. Adjust the volume of your stock solution with TE or H_{2}O to
obtain the desired molar or weight concentration.
