Application of Microchip Electrophoresis in the Analysis of RNA Aptamer-Protein Interactions

DNA and RNA can be separated by microchip electrophoresis (ME) and detected using an intercalating fluorescent dye. The advantages of this method are short sensing times (< 3 min), avoidance of a radioisotope labeling detection system, relatively low costs, and reduced labor intensity. In the present study, RNA aptamer-protein or -peptide interactions were analyzed using ME and the regression of free aptamers corresponding to unbound RNA was detected as the target protein or peptide increased in a dose-dependent manner. Our results demonstrate the applicability of this method to simple, rapid ligand screening in the interactions between oligonucleotides and their targets.

Keywords:

• In vitro selection
• Microchip electrophoresis
• RNA aptamer
• SYBR gold

Acknowledgments

We thank Dr. K. Ohno and Mr. C. Nakata (Showa University, Japan) for help with the experimental technique. We also thanks Mr. H. Nishijima (KAINOS Laboratories, Inc., Japan) for supporting ME instrument. We gratefully acknowledge Mr. S. Sekiya and Dr. P. K. R. Kumar for providing ΔNS3 and the RE peptide.

This article is dedicated to Professor Eiko Ohtsuka on the occasion of her 70th birthday.