Separation of pd(GC)12 from pd(AT)12 by free solution capillary electrophoresis.

The two synthetic self complementary oligonucleotides pd(AT)12 and pd(GC)12 were separated by free solution capillary electrophoresis (CZE) using simple borate buffers. The effects of pH (7.5-9) and the concentration of the buffer (0.03-0.35 M) were investigated. Higher pH values and buffer concentrations led to better resolution and longer migration times, the pH having a more pronounced effect on the separation than the concentration of the buffer. It is proposed that the conformation and effective length of the oligonucleotides may have a role in their separation in free solution capillary electrophoresis.