Aptamers are single stranded DNA or RNA molecules that fold into a secondary structure that generates high affinity and selectivity for particular target molecules. Aptamers have gained widespread attention for their potential as drug or diagnostic candidates. Unfortunately, the process for isolating aptamers remains technically challenging and time consuming. We have made advances in these areas with the introduction of capillary electrophoresis based aptamer selections (CE-SELEX) but room for further improvement remains.

In micro free flow electrophoresis (µFFE), a thin stream of sample is continuously introduced into a planar, microfluidic flow chamber. An electric field is applied perpendicularly to the flow through the separation chamber. Analytes are deflected laterally in the electric field according to their electrophoretic mobility. Preparative separations can be performed by continuously collecting fractions at the exit of the flow chamber.

µFFE is in many respects an ideal separation technique for isolating binding aptamers from large random sequence nucleic acid libraries. The target is incubated with the library and pumped into the separation chamber. Binding sequences are separated from nonbinders laterally in the separation chamber and collected as a separate fraction. The continuous nature of the separation allows large numbers of sequences to be separated without using extreme library concentrations. The continuous separation also eliminates the precise timing required for successful fraction collection in CE-SELEX.