Can I use the Nanodrop® to measure the concentration of synthetic oligonucleotides?
Nanodrop® technology can be used to measure the concentration of individual synthetic oligos using each oligonucleotide's unique analysis constant. By default, the Nanodrop equipment uses a value of "33" as a general constant for all single-stranded DNA, which is inappropriate for synthetic DNA. Oligonucleotides purchased through LGC Biosearch Technologies arrive with data sheets containing the extinction coefficient and molecular weight of each oligonucleotide. These numbers are used to calculate the analysis constant needed for Nanodrop concentration calculations.
Use the formula below to calculate the Analysis Constant (AC):
AC = (1/extinction coefficient) x (Molecular Weight (protonated)) x 1000 = AC in micrograms per OD260nm
We have determined through internal research that when measuring labeled oligonucleotides, the Nanodrop's linear range of detection is much more limited than advertised. For oligonucleotide stocks in the 100 µM range, the Nanodrop will record an apparent concentration that is significantly below the actual concentration. For accurate measurements, we recommend diluting 100 µM stocks by 25-fold to achieve a concentration in the range of 4 µM.