Extinction (absorption) coefficients of nucleic acids calculated at 260 nm

The most accurate method is based on the nearest-neighbor model and its published parameters^1,2 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 shown^3,4,5 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)].

DNA		RNA
Stack or monomer	Extinction coefficient	Stack or monomer	Extinction coefficient
pdA	15400	pA	15400
pdC	7400	pC	7200
pdG	11500	pG	11500
pdT	8700	pU	9900
dApdA	27400	ApA	27400
dApdC	21200	AdC	21000
dApdG	25000	ApG	25000
dApdT	22800	ApU	24000
dCpdA	21200	CpA	21000
dCpdC	14600	CpC	14200
dCpdG	18000	CpG	17800
dCpdT	15200	CpU	16200
dGpdA	25200	GpA	25200
dGpdC	17600	GpC	17400
dGpdG	21600	GpG	21600
dGpdT	20000	GpU	21200
dTpdA	23400	UpA	24600
dTpdC	16200	UpC	17200
dTpdG	19000	UpG	20000
dTpdT	16800	UpU	19600

Extinction coefficients are typically used to determine oligonucleotide concentrations from the Lambert-Beer law,

The extinction coefficient of any duplex DNA (ε_D) is less than the sum of the extinction coefficients of its complementary strands (ε_S1, ε_S2). This hypochromicity effect⁶ can be taken into account,

where f_AT and f_GC 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.

1. Cantor C.R., Warshaw M.M., and Shapiro H. (1970) Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides, Biopolymers 9, 1059-1077.
2. Fasman, G.D. (Ed.) (1975) Handbook of Biochemistry and Molecular Biology, Volume 1: Nucleic Acids, pp 589, 3rd edition, CRC Press.
3. Kallansrud G., and Ward B. (1996) A comparison of measured and calculated single- and double-stranded oligodeoxynucleotide extinction coefficients, Anal. Biochem. 236, 134-138.
4. Murphy J.H, and Trapane T.L. (1996) Concentration and extinction coefficient determination for oligonucleotides and analogs using a general phosphate analysis, Anal. Biochem. 240, 273-282.
5. Cavaluzzi M.J., and Borer P.N. (2004) Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA, Nucleic Acids Res. 32, e13.
6. Tataurov A.V., You Y., and Owczarzy R. (2008) Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids, Biophys. Chem. 133, 66-70.