Biophysics and Physicobiology
Online ISSN : 2189-4779
ISSN-L : 2189-4779
Regular Article
Prediction of the secondary structure of short DNA aptamers
Arina AfanasyevaChioko NagaoKenji Mizuguchi
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JOURNAL FREE ACCESS
Supplementary material

2019 Volume 16 Pages 287-294

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Abstract

Aptamers have a spectrum of applications in biotechnology and drug design, because of the relative simplicity of experimental protocols and advantages of stability and specificity associated with their structural properties. However, to understand the structure-function relationships of aptamers, robust structure modeling tools are necessary. Several such tools have been developed and extensively tested, although most of them target various forms of biological RNA. In this study, we tested the performance of three tools in application to DNA aptamers, since DNA aptamers are the focus of many studies, particularly in drug discovery. We demonstrated that in most cases, the secondary structure of DNA can be reconstructed with acceptable accuracy by at least one of the three tools tested (Mfold, RNAfold, and CentroidFold), although the G-quadruplex motif found in many of the DNA aptamer structures complicates the prediction, as well as the pseudoknot interaction. This problem should be addressed more carefully to improve prediction accuracy.

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© 2019 THE BIOPHYSICAL SOCIETY OF JAPAN
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