Electrophoretic separation of DNA using a new matrix in uncoated capillaries

A new separation matrix, consisting of polymer poly(N-isopropylacrylamide) (PNIPAM) and small molecule additive mannitol, was used for double-stranded (ds) DNA and plasmid DNA separation by capillary electrophoresis. The matrix had a low viscosity, which made it very easy to handle. The additive mannitol dramatically enhanced the sieving performance of PNIPAM in TBE buffer. The optimal mannitol concentration 6% in polymer solution, was determined with the consideration of both speed and resolution. A resolution of 0.95 was achieved on the separation of 271/281 bp in the ΦX174/HaeIII digest by using 1.5% PNIPAM + 6% mannitol, while the supercoiled, linear and nicked conformers of λ plasmid were separated in 1% PNIPAM + 6% mannitol, demonstrating the potential use of this new matrix for effective DNA separations. The dramatic impact of mannitol on sieving performance of PNIPAM solution was investigated. pH dependent self-coating ability of PNIPAM was revealed. The presence of mannitol in TBE buffer decreased the pH of the buffer, which led to more efficient self-coating ability of PNIPAM probable due to the formation of hydrogen bonds between PNIPAM molecules and silanol groups at the silica wall.