Separation of DNA Oligonucleotides Using Denaturing Urea PAGE

  • Fiona Flett
  • Heidrun Interthal
Part of the Methods in Molecular Biology book series (MIMB, volume 1054)


Denaturing urea polyacrylamide gel electrophoresis (PAGE) allows the separation of linear single-stranded DNA molecules based on molecular weight. This method can be used to analyze or purify short synthesized DNA oligonucleotides or products from enzymatic reactions.

In this chapter we describe how to prepare and how to run these high concentration polyacrylamide gels. We detail how to transfer a gel onto Whatman paper and how to dry it. Radiolabelled oligonucleotides are visualized by PhosphorImager technology.

Key words

Urea Formamide Sequencing gel DNA oligonucleotide Denaturing PAGE Tdp1 


  1. 1.
    Maniatis T, Jeffrey A, van deSande H (1975) Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry 14:3787–3794PubMedCrossRefGoogle Scholar
  2. 2.
    Interthal H, Chen HJ, Champoux JJ (2005) Human Tdp1 cleaves a broad spectrum of substrates, including phosphoamide linkages. J Biol Chem 280:36518–36528PubMedCrossRefGoogle Scholar
  3. 3.
  4. 4.
    Interthal H, Pouliot JJ, Champoux JJ (2001) The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the phospholipase D superfamily. Proc Natl Acad Sci U S A 98:12009–12014PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2013

Authors and Affiliations

  • Fiona Flett
    • 1
  • Heidrun Interthal
    • 1
  1. 1.Institute of Cell BiologyUniversity of EdinburghEdinburghUK

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