Prediction of the secondary structure of short DNA aptamers
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, ro...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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The Biophysical Society of Japan
2019-11-01
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| Series: | Biophysics and Physicobiology |
| Subjects: | |
| Online Access: | https://doi.org/10.2142/biophysico.16.0_287 |
| _version_ | 1818288248161566720 |
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| author | Arina Afanasyeva Chioko Nagao Kenji Mizuguchi |
| author_facet | Arina Afanasyeva Chioko Nagao Kenji Mizuguchi |
| author_sort | Arina Afanasyeva |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T01:53:22Z |
| format | Article |
| id | doaj.art-81bc65a3e3bc43839fd0a8ea0e8051ed |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-12-13T01:53:22Z |
| publishDate | 2019-11-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-81bc65a3e3bc43839fd0a8ea0e8051ed2022-12-22T00:03:27ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792019-11-011610.2142/biophysico.16.0_287Prediction of the secondary structure of short DNA aptamersArina Afanasyeva0Chioko Nagao1Kenji Mizuguchi2Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, JapanLaboratory of In-silico Drug Design, Center for Drug Design Research (CDDR), National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, JapanArtificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, JapanAptamers 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.https://doi.org/10.2142/biophysico.16.0_287g-quadruplexdot-bracket notationtanimoto similarity |
| spellingShingle | Arina Afanasyeva Chioko Nagao Kenji Mizuguchi Prediction of the secondary structure of short DNA aptamers Biophysics and Physicobiology g-quadruplex dot-bracket notation tanimoto similarity |
| title | Prediction of the secondary structure of short DNA aptamers |
| title_full | Prediction of the secondary structure of short DNA aptamers |
| title_fullStr | Prediction of the secondary structure of short DNA aptamers |
| title_full_unstemmed | Prediction of the secondary structure of short DNA aptamers |
| title_short | Prediction of the secondary structure of short DNA aptamers |
| title_sort | prediction of the secondary structure of short dna aptamers |
| topic | g-quadruplex dot-bracket notation tanimoto similarity |
| url | https://doi.org/10.2142/biophysico.16.0_287 |
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