High-Efficiency DNA Separation by Capillary Electrophoresis in a Polymer Solution with Ultralow Viscosity

Abstract

The viscosities of some polymer solutions for DNA separation in capillary electrophoresis are generally very high, which makes them hard to pump into the capillaries. We have developed a novel sieving buffer, based on low-molecular-weight hydroxypropylmethylcellulose, to separate DNA fragments. The viscosity of this sieving matrix was at least 1 order of magnitude lower than that of traditional buffers with similar sieving effect. The influence of additives such as urea and mannitol was investigated. It was found that the double-stranded DNA (ds DNA) fragments began to denature in 3.5 M urea, and 7 M urea can denature the ds DNA completely. The presence of mannitol will decrease the overlap threshold of the polymer solution (the concentration at which the polymer molecules begin to entangle with each other), which makes it possible to separate DNA fragments in a polymer solution of relatively low concentration. The influence of the electrical field was also investigated, and it was found that the mobility of DNA fragments up to 2000 bp in length did not change greatly with different electric fields. This phenomenon implies that the DNA fragments at this range do not change their conformation with the increase of electric field as was previously believed. The possible mechanism for the separation of DNA fragments is also discussed.