Electrophoretic separation of small DNA fragments in the presence of electroosmotic flow using poly(ethylene oxide) solutions

A new and simple method was demonstrated for separating φX-174/Hae III DNA restriction fragments and DNA markers V and VI, respectively, without filling capillaries with polymer solutions prior to analysis. Using this novel method, poly(ethylene oxide) (PEO) solutions containing ethidium bromide migrated into capillaries by electroosmotic flow (EOF) during the separation. Two DNA fragments (123 and 124 bp) in markers V and VI were well- resolved. RSD values for the separation of φX-174/Hae III DNA restriction fragments were less than 0.52% for 3 runs using a single 75-μm capillary and less than 3.96% using three different 75-μm capillaries. A highly viscous polymer solution prepared from 3% PEO was also used for separation of DNA markers V and VI. Theoretical plates up to 11.91 million/m and separation times of less than 7 min were achieved in the separation of φX-174/Hae III DNA restriction fragments using a 10-μm capillary and a 2% PEO solution. Advantages of this method include simplicity, short separation times, the ability to use highly viscous polymer solutions for separating small DNA fragments, and the possibility of introducing several different polymer solutions into capillaries to extend the DNA separation range.