title: DNA and buffers: the hidden danger of complex formation.
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.
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: N C
authors.initials: NC
authors.lastname: Stellwagen
authors.forename: C
authors.initials: C
authors.lastname: Gelfi
authors.forename: P G
authors.initials: PG
authors.lastname: Righetti
mesh_terms: D000085:Acetates / Q000378:metabolism / Q000494:pharmacology*; D001881:Borates / Q000378:metabolism / Q000494:pharmacology; D001888:Boric Acids / Q000378:metabolism / Q000494:pharmacology*; D002021:Buffers; D004247:DNA / Q000378:metabolism*; D004492:Edetic Acid / Q000378:metabolism / Q000494:pharmacology*; D004586:Electrophoresis / Q000009:adverse effects / Q000592:standards; D005029:Ethylenediamines / Q000378:metabolism / Q000494:pharmacology*; D005782:Gels; D014325:Tromethamine / Q000378:metabolism / Q000494:pharmacology*
chemical_list: D000085:Acetates; D001881:Borates; D001888:Boric Acids; D002021:Buffers; D005029:Ethylenediamines; D005782:Gels; C069591:Tris-borate-EDTA buffer; C115179:tris-acetate-EDTA buffer; D014325:Tromethamine; D004247:DNA; D004492:Edetic Acid