Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors

Abstract Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have b...

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Autores principales:	Iman Jeddi, Leonor Saiz
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4a7f7c6743fd42dca0fc7a53f99f386d
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spelling	oai:doaj.org-article:4a7f7c6743fd42dca0fc7a53f99f386d2021-12-02T12:30:13ZThree-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors10.1038/s41598-017-01348-52045-2322https://doaj.org/article/4a7f7c6743fd42dca0fc7a53f99f386d2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01348-5https://doaj.org/toc/2045-2322Abstract Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility. DNA aptamers are more stable than their RNA counterparts for biomedical applications but have the disadvantage of lacking the wide array of computational tools for RNA structural prediction. Here, we present the first approach to predict from sequence the three-dimensional structures of single stranded (ss) DNA required for aptamer applications, focusing explicitly on ssDNA hairpins. The approach consists of a pipeline that integrates sequentially building ssDNA secondary structure from sequence, constructing equivalent 3D ssRNA models, transforming the 3D ssRNA models into ssDNA 3D structures, and refining the resulting ssDNA 3D structures. Through this pipeline, our approach faithfully predicts the representative structures available in the Nucleic Acid Database and Protein Data Bank databases. Our results, thus, open up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors.Iman JeddiLeonor SaizNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Iman Jeddi Leonor Saiz Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
description	Abstract Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility. DNA aptamers are more stable than their RNA counterparts for biomedical applications but have the disadvantage of lacking the wide array of computational tools for RNA structural prediction. Here, we present the first approach to predict from sequence the three-dimensional structures of single stranded (ss) DNA required for aptamer applications, focusing explicitly on ssDNA hairpins. The approach consists of a pipeline that integrates sequentially building ssDNA secondary structure from sequence, constructing equivalent 3D ssRNA models, transforming the 3D ssRNA models into ssDNA 3D structures, and refining the resulting ssDNA 3D structures. Through this pipeline, our approach faithfully predicts the representative structures available in the Nucleic Acid Database and Protein Data Bank databases. Our results, thus, open up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors.
format	article
author	Iman Jeddi Leonor Saiz
author_facet	Iman Jeddi Leonor Saiz
author_sort	Iman Jeddi
title	Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
title_short	Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
title_full	Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
title_fullStr	Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
title_full_unstemmed	Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
title_sort	three-dimensional modeling of single stranded dna hairpins for aptamer-based biosensors
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/4a7f7c6743fd42dca0fc7a53f99f386d
work_keys_str_mv	AT imanjeddi threedimensionalmodelingofsinglestrandeddnahairpinsforaptamerbasedbiosensors AT leonorsaiz threedimensionalmodelingofsinglestrandeddnahairpinsforaptamerbasedbiosensors
_version_	1718394394597392384

Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors

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