DNA and buffers: The hidden danger of complex formation

Nancy C. Stellwagen, Cecilia Gelfi, Pier Giorgio Righetti

Research output: Contribution to journalArticle

Abstract

The free solution electrophoretic mobility of DNA differs significantly in different buffers, suggesting that DNA-buffer interactions are present in certain buffer systems. Here, capillary and gel electrophoresis data are combined to show that the Tris ions in Tris-acetate-EDTA (TAE) buffers are associated with the DNA helix to approximately the same extent as sodium ions. The borate ions in Tris-borate-EDTA (TBE) buffers interact with DNA to form highly charged DNA-borate complexes, which are stable both in free solution and in polyacrylamide gels. DNA-borate complexes are not observed in agarose gels, because of the competition of the agarose gel fibers for the borate residues. The resulting agarose-borate complexes increase the negative charge of the agarose gel fibers, leading to an increased electroendosmotic flow of the solvent in agarose-TBE gels. The combined results indicate that the buffers in which DNA is studied cannot automatically be assumed to be innocuous. (C) 2000 John Wiley and Sons, Inc.

Original languageEnglish
Pages (from-to)137-142
Number of pages6
JournalBiopolymers
Volume54
Issue number2
DOIs
Publication statusPublished - 2000

Keywords

  • Agarose gels
  • DNA
  • DNA capillary electrophoresis
  • DNA gel electrophoresis
  • DNA-borate complexes
  • Electroendosmotic flow

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

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