NMR monitoring of the SELEX process to confirm enrichment of structured RNA

Abstract RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplificat...

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Autores principales:	Ryo Amano, Kazuteru Aoki, Shin Miyakawa, Yoshikazu Nakamura, Tomoko Kozu, Gota Kawai, Taiichi Sakamoto
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a719e1e805e04e56860ef285c5f3fcd1
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spelling	oai:doaj.org-article:a719e1e805e04e56860ef285c5f3fcd12021-12-02T16:06:15ZNMR monitoring of the SELEX process to confirm enrichment of structured RNA10.1038/s41598-017-00273-x2045-2322https://doaj.org/article/a719e1e805e04e56860ef285c5f3fcd12017-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00273-xhttps://doaj.org/toc/2045-2322Abstract RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.Ryo AmanoKazuteru AokiShin MiyakawaYoshikazu NakamuraTomoko KozuGota KawaiTaiichi SakamotoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ryo Amano Kazuteru Aoki Shin Miyakawa Yoshikazu Nakamura Tomoko Kozu Gota Kawai Taiichi Sakamoto NMR monitoring of the SELEX process to confirm enrichment of structured RNA
description	Abstract RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.
format	article
author	Ryo Amano Kazuteru Aoki Shin Miyakawa Yoshikazu Nakamura Tomoko Kozu Gota Kawai Taiichi Sakamoto
author_facet	Ryo Amano Kazuteru Aoki Shin Miyakawa Yoshikazu Nakamura Tomoko Kozu Gota Kawai Taiichi Sakamoto
author_sort	Ryo Amano
title	NMR monitoring of the SELEX process to confirm enrichment of structured RNA
title_short	NMR monitoring of the SELEX process to confirm enrichment of structured RNA
title_full	NMR monitoring of the SELEX process to confirm enrichment of structured RNA
title_fullStr	NMR monitoring of the SELEX process to confirm enrichment of structured RNA
title_full_unstemmed	NMR monitoring of the SELEX process to confirm enrichment of structured RNA
title_sort	nmr monitoring of the selex process to confirm enrichment of structured rna
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/a719e1e805e04e56860ef285c5f3fcd1
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_version_	1718385044373897216

NMR monitoring of the SELEX process to confirm enrichment of structured RNA

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