UV spectrum of DNA calculator
Frequently Asked Questions
Can I predict spectrum of RNA?
No. Only sequences containing standard DNA bases (A, T, C, and G) can be calculated.
Has the algorithm been published?
The extinction coefficient of DNA is calculated from the nearest-neighbor model at 260 nm. The parameters are reported in the following publications:
- 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.
Hypochromicity and extinction coefficients at other wavelengths are predicted using parameters from:
Please use this publication to reference results of web server calculations.
What is the percent error of the predictions?
Will the extinction coefficient change with pH and solvent composition?
Yes. The predicted extinction coefficient is accurate in pH range from 6.5 to 8.5. When oligonucleotide absorbance is measured, it is therefore recommended to use a low salt buffer (several mM sodium phosphate or Tris) to maintain neutral pH. Single stranded oligodeoxynucleotides may also fold into secondary structures in solutions of high concentrations of cations, and this will decrease their extinction coefficient. Metal cations that bind to bases (Cu2+
) can dramatically change DNA extinction coefficient (Sissoëff I., Grisvard J., Guilllé E. (1978) Studies on metal ions-DNA interactions: Specific behaviour of reiterative DNA sequences. Prog. Biophys. Molec. Biol.
, 31: 165-199). Magnesium cations associate mostly with negatively charged phosphate backbone groups. Mg2+
ions are known to slightly decrease DNA extinction coefficient (5-10%).
Extinction coefficients of double stranded DNAs were measured in 120mM NaCl/Na-phosphate buffer. Under those conditions, the duplex form was stable. Duplexes could denature in buffers of lower salt concentrations - the extinction coefficient of duplexes would not be relevant in this case.
What is the Cavaluzzi-Borer correction?
Cavaluzzi and Borer measured the extinction coefficients of mononucleotides using a novel NMR method (Cavaluzzi, Borer (2004) Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA. Nucleic Acids Res.
, 32: e13). This correction changes extinction coefficients up to 6% and could improve accuracy of predictions.
How can I copy the table of wavelengths and extinction coefficients?
If copy and paste does not replicate table format, try a different web browser. For example, Internet Explorer 8 will copy results as a table.