Analytical Sciences

Fractionation of Single-stranded DNAs with/without Stable Preorganized Structures Using Capillary Sieving Electrophoresis for Aptamer Selection

Masahide WADA,* Tatsuro ENDO,* Hideaki HISAMOTO,* and Kenji SUEYOSHI*,**

*Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen, Naka, Sakai, Osaka 599-8531, Japan
**PRESTO, Japan Science and Technology Agency, Tokyo 102-0076, Japan

Aptamers, single-stranded DNAs/RNAs with a strong and specific interaction towards a target molecule, have wide applications in the fields of medicine and biosensors. In conventional aptamer selection methods, it is difficult to obtain “preorganized” and/or “induced-fit” type of aptamers selectively. In this study, separation and fractionation of single-stranded DNAs with/without stable preorganized structures were carried out using capillary sieving electrophoresis. The fractionated DNAs showed different mobilities and thermodynamic stabilities of their secondary structures; this outcome is deemed to be necessary for the synthesis of novel aptasensors with a desirable sensing mechanism.

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