The most accurate method is based on the nearest-neighbor model and its published parameters1,2 for DNA and RNA. These parameters are presented in the table below and were determined at wavelength of 260 nm, 25 degrees of Celsius, and neutral pH. The average error of calculated extinction coefficients was shown3,4,5 to be around 4 % under these conditions. For example, the extinction coefficient (ε) of linear oligonucleotide 5'-dATGCTTC-3' is,
When this DNA oligomer is circularized, the extinction coefficient is predicted using the following equation,
The following table contains extinction coefficients [liter/(mol.cm)].
|Stack or monomer||Extinction coefficient||Stack or monomer||Extinction coefficient|
Extinction coefficients are typically used to determine oligonucleotide concentrations from the Lambert-Beer law,
The extinction coefficient of any duplex DNA (εD) is less than the sum of the extinction coefficients of its complementary strands (εS1, εS2). This hypochromicity effect6 can be taken into account,
where fAT and fGC are fractions of AT and GC base pairs, respectively.
We have developed an on-line calculator6 that predicts oligonucleotide UV spectrum as well as extinction coefficients for both single-stranded and double-stranded DNAs. Click here to run calculations at IDT Biophysics website.