We have developed the method^{1} that predicts oligonucleotide
UV spectrum as well as extinction coefficients for both single-stranded and double-stranded DNAs.
The most accurate approach is based on the nearest-neighbor model and its
published parameters^{2,3} for DNA and RNA. These parameters are presented in the table below
and were determined **at wavelength of 260 nm, and neutral pH**.
The average error of calculated extinction coefficients was shown^{4,5,6} to be
around 4 % under these conditions.
For example, the extinction coefficient (ε) of linear oligonucleotide 5'-dATGCTTC-3' is,

If any modifying chemical group is attached to an oligonucleotide, extinction coefficient of the group needs to be added.

The table of extinction coefficients [liter/(mol.cm)] for DNA and RNA oligonucleotides.

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,

Absorbance of single stranded oligonucleotide is typically measured in a buffer of neutral pH
and low salt concentrations (less than 10mM). High concentrations of cations may promote oligonucleotide
folding. This is even more likely for RNA oligonucleotides, therefore, it is recommended to disrupt folding
by heating up solution to temperature of 85^{o}C for absorbance measurements^{7}.

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 effect^{1}
can be taken into account,

where *f*_{AT} and *f*_{GC} are fractions of AT and GC base pairs, respectively.

References

- 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. - 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. - Fasman, G.D. (Ed.) (1975)
*Handbook of Biochemistry and Molecular Biology, Volume 1: Nucleic Acids*, pp 589, 3rd edition, CRC Press. - Kallansrud G., and Ward B. (1996) A comparison of measured and calculated
single- and double-stranded oligodeoxynucleotide extinction coefficients,
*Anal. Biochem. 236*, 134-138. - 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. - 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. - Xia T., SantaLucia J., Jr., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox C.,
and Turner D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model
for formation of RNA duplexes with Watson-Crick base pairs,
*Biochemistry 37*, 14719-14735.

Copyright 2019, Updated April 2, 2019 version 5.14.