Few studies were performed to investigate the molecular recognition capabilities of hybridized aptamers. This study is aimed at applying both theoretical algorithms and experimental assays to examine the effects of hybridization length and region on the secondary structures and binding functionality of hybridized aptamers. The experimental results were significantly different from the structural predictions in many hybridization conditions. To explain this difference, we further proposed a novel equilibrium reaction model that can explicitly analyze the molecular interactions between hybridized aptamers and their targets. We believe that the research findings and the novel model can be used to guide numerous hybridized aptamer-based applications.
2010 John Wiley & Sons, Ltd.