title: Microarrays for identifying binding sites and probing structure of RNAs.
abstract: 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.
authors.affiliation: Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland.
authors.forename: Ryszard
authors.initials: R
authors.lastname: Kierzek
authors.affiliation: Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
authors.affiliation: Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland elzbieta.kierzek@ibch.poznan.pl.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Kierzek
mesh_terms: D001665:Binding Sites; D049673:History, 20th Century; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis / Q000266:history; D012313:RNA / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012313:RNA