Microarrays for identifying binding sites and probing structure of RNAs

Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods f...

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Main Authors:	Kierzek, Ryszard, Turner, Douglas H., Kierzek, Elzbieta
Format:	Online
Language:	English
Published:	Oxford University Press 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288193/

id	pubmed-4288193
recordtype	oai_dc
spelling	pubmed-42881932015-02-19 Microarrays for identifying binding sites and probing structure of RNAs Kierzek, Ryszard Turner, Douglas H. Kierzek, Elzbieta Survey and Summary Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure–function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs. Oxford University Press 2015-01-09 2014-12-12 /pmc/articles/PMC4288193/ /pubmed/25505162 http://dx.doi.org/10.1093/nar/gku1303 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Kierzek, Ryszard Turner, Douglas H. Kierzek, Elzbieta
spellingShingle	Kierzek, Ryszard Turner, Douglas H. Kierzek, Elzbieta Microarrays for identifying binding sites and probing structure of RNAs
author_facet	Kierzek, Ryszard Turner, Douglas H. Kierzek, Elzbieta
author_sort	Kierzek, Ryszard
title	Microarrays for identifying binding sites and probing structure of RNAs
title_short	Microarrays for identifying binding sites and probing structure of RNAs
title_full	Microarrays for identifying binding sites and probing structure of RNAs
title_fullStr	Microarrays for identifying binding sites and probing structure of RNAs
title_full_unstemmed	Microarrays for identifying binding sites and probing structure of RNAs
title_sort	microarrays for identifying binding sites and probing structure of rnas
description	Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure–function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs.
publisher	Oxford University Press
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288193/
_version_	1613174648019615744

Microarrays for identifying binding sites and probing structure of RNAs

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