Separation of double- and single-stranded DNA restriction fragments: Capillary electrophoresis with polymer solutions under alkaline conditions

Capillary electrophoresis in buffers containing hydroxyethyl cellulose (HEC ) was used to separate double- and single-stranded DNA restriction fragment s under neutral and alkaline conditions in epoxy-coated capillaries. It was found that better resolution was achieved using highly entangled NEC solut ions for a narrow range of DNA fragment sizes, while lower resolution was o btained over a wide separation range using diluted HEC solutions. Optimal r esolution of these DNA fragments was obtained using buffers containing 0.5% HEC at pH 11 with plate numbers exceeding 3 x 10(6) plates/m. It was also found that the diffusion coefficients and electrophoretic mobilities of DNA fragments decreased with increasing pH. This may indicate a more extended DNA conformation and, therefore, enhancement of transient entanglement coup ling between DNA and HEC polymers under alkaline condition. At pH 12, ss-DN A were well separated in entangled HEC solutions; however, the resolution o f ss-DNA was significantly decreased in diluted polymer solution.