Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

Abstract Aptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs—including different aptamer-attachment ends, aptamer surface densities, aptamer orie...

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Autores principales:	Iman Jeddi, Leonor Saiz
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cdf59dc121e4481ab88b7ff2f44f5cd2
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spelling	oai:doaj.org-article:cdf59dc121e4481ab88b7ff2f44f5cd22021-12-02T14:42:21ZComputational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate10.1038/s41598-021-88796-22045-2322https://doaj.org/article/cdf59dc121e4481ab88b7ff2f44f5cd22021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88796-2https://doaj.org/toc/2045-2322Abstract Aptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs—including different aptamer-attachment ends, aptamer surface densities, aptamer orientations, and solvent solutions—and applied it to an anti MUC1 aptamer tethered to a silica biosensor substrate. Amongst all the system designs explored, we found that attaching the anti MUC1 aptamer through the 5′ terminal end, in a high surface density configuration, and solvated in a 0.8 M NaCl solution provided the best exposure of the aptamer MUC1 binding regions and resulted in the least amount of aptamer backbone fluctuations. Many of the other designs led to non-functional systems, with the aptamer collapsing onto the surface. The computational approach we have developed and the resulting analysis techniques can be employed for the rational design of aptamer-based biosensors and provide a valuable tool for improving biosensor performance and repeatability.Iman JeddiLeonor SaizNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Iman Jeddi Leonor Saiz Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate
description	Abstract Aptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs—including different aptamer-attachment ends, aptamer surface densities, aptamer orientations, and solvent solutions—and applied it to an anti MUC1 aptamer tethered to a silica biosensor substrate. Amongst all the system designs explored, we found that attaching the anti MUC1 aptamer through the 5′ terminal end, in a high surface density configuration, and solvated in a 0.8 M NaCl solution provided the best exposure of the aptamer MUC1 binding regions and resulted in the least amount of aptamer backbone fluctuations. Many of the other designs led to non-functional systems, with the aptamer collapsing onto the surface. The computational approach we have developed and the resulting analysis techniques can be employed for the rational design of aptamer-based biosensors and provide a valuable tool for improving biosensor performance and repeatability.
format	article
author	Iman Jeddi Leonor Saiz
author_facet	Iman Jeddi Leonor Saiz
author_sort	Iman Jeddi
title	Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate
title_short	Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate
title_full	Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate
title_fullStr	Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate
title_full_unstemmed	Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate
title_sort	computational design of single-stranded dna hairpin aptamers immobilized on a biosensor substrate
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cdf59dc121e4481ab88b7ff2f44f5cd2
work_keys_str_mv	AT imanjeddi computationaldesignofsinglestrandeddnahairpinaptamersimmobilizedonabiosensorsubstrate AT leonorsaiz computationaldesignofsinglestrandeddnahairpinaptamersimmobilizedonabiosensorsubstrate
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Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

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