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. 2010 Mar;38(4):e21.
doi: 10.1093/nar/gkp1101. Epub 2009 Dec 2.

Selection of DNA aptamers using atomic force microscopy

Yusuke Miyachi  1 , Nobuaki Shimizu, Chiaki Ogino, Akihiko Kondo
Affiliations

Selection of DNA aptamers using atomic force microscopy

Yusuke Miyachi et al. Nucleic Acids Res. 2010 Mar.

Abstract

Atomic force microscopy (AFM) can detect the adhesion or affinity force between a sample surface and cantilever, dynamically. This feature is useful as a method for the selection of aptamers that bind to their targets with very high affinity. Therefore, we propose the Systematic Evolution of Ligands by an EXponential enrichment (SELEX) method using AFM to obtain aptamers that have a strong affinity for target molecules. In this study, thrombin was chosen as the target molecule, and an 'AFM-SELEX' cycle was performed. As a result, selected cycles were completed with only three rounds, and many of the obtained aptamers had a higher affinity to thrombin than the conventional thrombin aptamer. Moreover, one type of obtained aptamer had a high affinity to thrombin as well as the anti-thrombin antibody. AFM-SELEX is, therefore, considered to be an available method for the selection of DNA aptamers that have a high affinity for their target molecules.

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Figures

Figure 1.
Figure 1.
The scheme of a new SELEX strategy for functional oligonucleotide screening by AFM.
Figure 2.
Figure 2.
Histogram of adhesion force between ssDNA and protein for 4096 data points. (A) adhesion force between 0 pool ssDNA and thrombin, (B) adhesion force between round 1 elution pool and thrombin, (C) adhesion force between round 2 elution pool and thrombin, (D) adhesion force between round 3 elution pool and thrombin and (E) the average of affinity force between each round elution pool and thrombin.
Figure 3.
Figure 3.
Affinity image between round 3 elution pool and thrombin showing the affinity images (A) as well as the topography images (B).
Figure 4.
Figure 4.
Histogram of the affinity force between aptamer and thrombin for 4096 data points. (A) TBA-1, (B) TBA-2, (C) conventional thrombin aptamer and (D) anti-thrombin antibody.
Figure 5.
Figure 5.
Binding curve of TBA-1 with thrombin. Each of thrombin solution (10−7–10−13 M) was mixed with TBA-1 (100 nM), and incubated for 2 h at room temperature. After incubation, the polarization was measured.
See this image and copyright information in PMC

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