Detection of structural changes of RNA aptamer containing GGA repeats under the ionic condition using the microchip electrophoresis

We performed in vitro selection against bovine prion protein (bPrP) using RNA pools with thirty-nucleotides randomized regions. Among the obtained RNA aptamers, RNA aptamer wt2 possessed four GGA triplets. It is known that RNA and DNA oligomers containing GGA repeat sequences show a G-quadruplex structure in the presence of K+ or Na+ ions using the NMR and crystallographic studies. Recently we have been studying RNA aptamer-protein, -peptide and -RNA interactions using microchip electrophoresis (ME). In this study, we used this system to detect structural changes of RNA aptamer wt2 in the presence of K+ and Na+ ions, and detected the dimer formation with simple operation.