Structural evaluation of the DNA aptamer for ATP DH25.42 by AFM

Atomic force microscopy (AFM) can dynamically detect the adhesion or affinity force between a sample surface and a cantilever. This feature could be used to analyze bio-molecular interactions between a DNA aptamer and a target molecule. In this study, the binding force between adenosine triphosphate (ATP) and the anti-ATP DNA aptamer DH25.42, based on structural changes was measured using AFM. In addition, the relationship between the cations in the binding buffer, and the affinity and structure formation of the DNA aptamer was also evaluated using AFM and circular dichroism (CD) spectrum analysis. As a result, the specific force between DH25.42 and ATP could be measured by AFM. Moreover, it was suggested that Mg(2+) in the binding buffer was critical to the binding function of DH25.42 to ATP.