Microarrays for Identifying Binding Sites and Probing Structure of RNAs

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2014 Dec 16

PMID 25505162

Citations 14

Authors

Ryszard Kierzek

Douglas H Turner

Elzbieta Kierzek

Affiliations

Soon will be listed here.

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.

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References

Augenlicht L, Kobrin D . Cloning and screening of sequences expressed in a mouse colon tumor. Cancer Res. 1982; 42(3):1088-93. View

Freier S, Kierzek R, Caruthers M, Neilson T, Turner D . Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry. 1986; 25(11):3209-13. DOI: 10.1021/bi00359a019. View

Sugimoto N, Kierzek R, Freier S, Turner D . Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry. 1986; 25(19):5755-9. DOI: 10.1021/bi00367a061. View

Kulesh D, Clive D, Zarlenga D, GREENE J . Identification of interferon-modulated proliferation-related cDNA sequences. Proc Natl Acad Sci U S A. 1987; 84(23):8453-7. PMC: 299562. DOI: 10.1073/pnas.84.23.8453. View

Sampson J, Uhlenbeck O . Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci U S A. 1988; 85(4):1033-7. PMC: 279695. DOI: 10.1073/pnas.85.4.1033. View

Fodor S, Read J, Pirrung M, Stryer L, Lu A, Solas D . Light-directed, spatially addressable parallel chemical synthesis. Science. 1991; 251(4995):767-73. DOI: 10.1126/science.1990438. View

Nazar R . Higher order structure of the ribosomal 5 S RNA. J Biol Chem. 1991; 266(7):4562-7. View

Ciesiollka J, Lorenz S, Erdmann V . Different conformational forms of Escherichia coli and rat liver 5S rRNA revealed by Pb(II)-induced hydrolysis. Eur J Biochem. 1992; 204(2):583-9. DOI: 10.1111/j.1432-1033.1992.tb16671.x. View

Maskos U, Southern E . Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ. Nucleic Acids Res. 1992; 20(7):1679-84. PMC: 312256. DOI: 10.1093/nar/20.7.1679. View

10.

Southern E, Maskos U, Elder J . Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. 1992; 13(4):1008-17. DOI: 10.1016/0888-7543(92)90014-j. View

11.

Maskos U, Southern E . A novel method for the parallel analysis of multiple mutations in multiple samples. Nucleic Acids Res. 1993; 21(9):2269-70. PMC: 309508. DOI: 10.1093/nar/21.9.2269. View

12.

Maskos U, Southern E . A study of oligonucleotide reassociation using large arrays of oligonucleotides synthesised on a glass support. Nucleic Acids Res. 1993; 21(20):4663-9. PMC: 331488. DOI: 10.1093/nar/21.20.4663. View

13.

Southern E, Elder J, Johnson M, Mir K, Wang L, Williams J . Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res. 1994; 22(8):1368-73. PMC: 307992. DOI: 10.1093/nar/22.8.1368. View

14.

Sugimoto N, Nakano S, Katoh M, Matsumura A, Nakamuta H, Ohmichi T . Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry. 1995; 34(35):11211-6. DOI: 10.1021/bi00035a029. View

15.

Schena M, Shalon D, Davis R, Brown P . Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995; 270(5235):467-70. DOI: 10.1126/science.270.5235.467. View

16.

SantaLucia Jr J, Allawi H, Seneviratne P . Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry. 1996; 35(11):3555-62. DOI: 10.1021/bi951907q. View

17.

Timofeev E, Kochetkova S, Mirzabekov A, Florentiev V . Regioselective immobilization of short oligonucleotides to acrylic copolymer gels. Nucleic Acids Res. 1996; 24(16):3142-8. PMC: 146065. DOI: 10.1093/nar/24.16.3142. View

18.

Michalowski D, Wrzesinski J, Ciesiolka J, Krzyzosiak W . Effect of modified nucleotides on structure of yeast tRNA(Phe). Comparative studies by metal ion-induced hydrolysis and nuclease mapping. Biochimie. 1996; 78(2):131-8. DOI: 10.1016/0300-9084(96)82645-9. View

19.

Maskos U, Southern E . Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation. Nucleic Acids Res. 1992; 20(7):1675-8. PMC: 312255. DOI: 10.1093/nar/20.7.1675. View

20.

Hoheisel J . Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet. 2006; 7(3):200-10. DOI: 10.1038/nrg1809. View