Richard Owczarzy
                           High-throughput DNA biophysics
 
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Calculation procedure for extinction (absorption) coefficient of DNA and RNA

The method is based on paper by Cantor C.R., Warshaw M.M., Shapiro, H, Biopolymers, 9, 1059-1077 (1970). The data are also shown at Handbook of Biochemistry and Molecular Biology, Volume 1: Nucleic Acids, Fasman, G.D. editor, page 589, 3rd edition, CRC Press, 1975. Extinction coefficient at 260 nm, 25 degrees of Celsius, and neutral pH for the single-strand DNA or RNA is predicted by the nearest-neighbor method. For example, the extinction coefficient of DNA oligomer 5'-dATGCTTC-3' is

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The following table contains extinction coefficients [liter/(mol.cm)].
DNARNA
Stack or monomerExtinction coefficientStack or monomerExtinction coefficient
pdA 15400pA 15400
pdC 7400pC 7200
pdG 11500pG 11500
pdT 8700pU 9900
dApdA27400ApA27400
dApdC21200AdC21000
dApdG25000ApG25000
dApdT22800ApU24000
dCpdA21200CpA21000
dCpdC14600CpC14200
dCpdG18000CpG17800
dCpdT15200CpU16200
dGpdA25200GpA25200
dGpdC17600GpC17400
dGpdG21600GpG21600
dGpdT20000GpU21200
dTpdA23400UpA24600
dTpdC16200UpC17200
dTpdG19000UpG20000
dTpdT16800UpU19600


Extinction coefficient is used to determine DNA oligomer concentration from Lambert-Beer law,

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Copyright 1996, Updated May 9, 2008, version 4.00