Interbase-FRET binding assay for pre-microRNAs

Abstract The aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small-molecule inhibitors of miR biogenesis. These inhibitors have the potential to (i) dissect miR mechanisms of action, (ii) discover new...

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Autores principales:	Mattias Bood, Anna Wypijewska del Nogal, Jesper R. Nilsson, Fredrik Edfeldt, Anders Dahlén, Malin Lemurell, L. Marcus Wilhelmsson, Morten Grøtli
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cda9c7e7160e4417b694ff5cf0c29da7
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spelling	oai:doaj.org-article:cda9c7e7160e4417b694ff5cf0c29da72021-12-02T16:55:54ZInterbase-FRET binding assay for pre-microRNAs10.1038/s41598-021-88922-02045-2322https://doaj.org/article/cda9c7e7160e4417b694ff5cf0c29da72021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88922-0https://doaj.org/toc/2045-2322Abstract The aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small-molecule inhibitors of miR biogenesis. These inhibitors have the potential to (i) dissect miR mechanisms of action, (ii) discover new drug targets, and (iii) function as new therapeutic agents. Here, we designed Förster resonance energy transfer (FRET)-labeled oligoribonucleotides of the precursor of the oncogenic miR-21 (pre-miR-21) and used them together with a set of aminoglycosides to develop an interbase-FRET assay to detect ligand binding to pre-miRs. Our interbase-FRET assay accurately reports structural changes of the RNA oligonucleotide induced by ligand binding. We demonstrate its application in a rapid, qualitative drug candidate screen by assessing the relative binding affinity between 12 aminoglycoside antibiotics and pre-miR-21. Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were used to validate our new FRET method, and the accuracy of our FRET assay was shown to be similar to the established techniques. With its advantages over SPR and ITC owing to its high sensitivity, small sample size, straightforward technique and the possibility for high-throughput expansion, we envision that our solution-based method can be applied in pre-miRNA–target binding studies.Mattias BoodAnna Wypijewska del NogalJesper R. NilssonFredrik EdfeldtAnders DahlénMalin LemurellL. Marcus WilhelmssonMorten GrøtliNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mattias Bood Anna Wypijewska del Nogal Jesper R. Nilsson Fredrik Edfeldt Anders Dahlén Malin Lemurell L. Marcus Wilhelmsson Morten Grøtli Interbase-FRET binding assay for pre-microRNAs
description	Abstract The aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small-molecule inhibitors of miR biogenesis. These inhibitors have the potential to (i) dissect miR mechanisms of action, (ii) discover new drug targets, and (iii) function as new therapeutic agents. Here, we designed Förster resonance energy transfer (FRET)-labeled oligoribonucleotides of the precursor of the oncogenic miR-21 (pre-miR-21) and used them together with a set of aminoglycosides to develop an interbase-FRET assay to detect ligand binding to pre-miRs. Our interbase-FRET assay accurately reports structural changes of the RNA oligonucleotide induced by ligand binding. We demonstrate its application in a rapid, qualitative drug candidate screen by assessing the relative binding affinity between 12 aminoglycoside antibiotics and pre-miR-21. Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were used to validate our new FRET method, and the accuracy of our FRET assay was shown to be similar to the established techniques. With its advantages over SPR and ITC owing to its high sensitivity, small sample size, straightforward technique and the possibility for high-throughput expansion, we envision that our solution-based method can be applied in pre-miRNA–target binding studies.
format	article
author	Mattias Bood Anna Wypijewska del Nogal Jesper R. Nilsson Fredrik Edfeldt Anders Dahlén Malin Lemurell L. Marcus Wilhelmsson Morten Grøtli
author_facet	Mattias Bood Anna Wypijewska del Nogal Jesper R. Nilsson Fredrik Edfeldt Anders Dahlén Malin Lemurell L. Marcus Wilhelmsson Morten Grøtli
author_sort	Mattias Bood
title	Interbase-FRET binding assay for pre-microRNAs
title_short	Interbase-FRET binding assay for pre-microRNAs
title_full	Interbase-FRET binding assay for pre-microRNAs
title_fullStr	Interbase-FRET binding assay for pre-microRNAs
title_full_unstemmed	Interbase-FRET binding assay for pre-microRNAs
title_sort	interbase-fret binding assay for pre-micrornas
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cda9c7e7160e4417b694ff5cf0c29da7
work_keys_str_mv	AT mattiasbood interbasefretbindingassayforpremicrornas AT annawypijewskadelnogal interbasefretbindingassayforpremicrornas AT jesperrnilsson interbasefretbindingassayforpremicrornas AT fredrikedfeldt interbasefretbindingassayforpremicrornas AT andersdahlen interbasefretbindingassayforpremicrornas AT malinlemurell interbasefretbindingassayforpremicrornas AT lmarcuswilhelmsson interbasefretbindingassayforpremicrornas AT mortengrøtli interbasefretbindingassayforpremicrornas
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Interbase-FRET binding assay for pre-microRNAs

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