DNA and buffers: Are there any noninteracting, neutral pH buffers?

The interaction of DNA with various neutral pH, amine-based buffers has bee n analyzed by free solution capillary electrophoresis, using a mixture of a plasmid-sized DNA molecule and a small DNA oligonucleotide as the reporter system. The two DNAs migrate as separate, nearly Gaussian-shaped peaks in 20-80 mM TAE (TAE, Tris-acetate-EDTA; Tris, tris[hydroxymethyl]aminomethane ) buffer. The separation between the peaks gradually increases with increas ing TAE buffer concentration because of differences in solvent friction bet ween large and small DNA molecules. The two DNAs form complexes with the be rate ions in TEE (Tris-borate-EDTA) buffer, with mobilities that depend on the DNA/borate ratio. In 45 mM TEE buffer, the two DNAs comigrate as a sing le sharp peak, with a mobility that is faster than either of the constituen t DNAs in the same buffer. Hence, the mixed DNA-borate complex is stabilize d by the binding of additional berate ions, possibly forming bridges betwee n the different DNAs. The mixed DNA-borate complex is gradually dissociated into its component DNAs by increasing the TEE concentration, possibly beca use the berate binding sites become saturated at high buffer concentrations . Other neutral pH, amine-based buffers, such as Mops (N-[N-morpholino]prop anesulfonic acid), Hepes (N'-[2-hydroxyethyl]piperazine,N'-[2-ethanesulfoni c acid]), Bes (N,N-bis[2-hydroxyethyl]-2-aminoethanesulfonic acid), Tes (N- tris[hydroxymethyl]methyl-2-aminoethanesulfonic acid), and tricine (N-tris[ hydroxymethyl]methylglycine) also form complexes with DNA, giving distorted peaks in the electropherograms. The combined results indicate that berate buffers and most neutral pH, amine-based buffers interact with DNA. (C) 200 0 Academic Press.