High efficiency DNA separation by capillary electrophoresis in a polymer solution with ultralow viscosity

The viscosities of some polymer solutions for DNA separation in capillary e lectrophoresis are generally very high, which makes them hard to pump into the capillaries. We have developed a novel sieving buffer, based on low-mol ecular-weight hydroxypropylmethylcellulose, to separate DNA fragments. The viscosity of this sieving matrix was at least I order of magnitude lower th an that of traditional buffers with similar sieving effect, The influence o f additives such as urea and mannitol was investigated. It was found that t he 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 w ill decrease the overlap threshold of the polymer solution (the concentrati on at which the polymer molecules begin to entangle with each other), which makes it possible to separate DNA fragments in a polymer solution of relat ively low concentration. The influence of the electrical held was also inve stigated, 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 phen omenon implies that the DNA fragments at this range do not change their con formation with the increase of electric field as was previously believed. T he possible mechanism for the separation of DNA fragments is also discussed .